Biology 1 study guide: Midterm 2.
Biology 1 study guide: Midterm 2. 01:119:115
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EXAM 2: STUDY GUIDE (LECTURES 9-17) Lecture 9: Photosynthesis: Lecture 10: Mitosis: Lecture 11: Meiosis: Lecture 12: Mendelian Genetics: Lecture 13: Chromosome: Lecture 14: DNA Technology: Lecture 15: Human Genetics: Lecture 16: Darwinian Evolution: Lecture 17: Microevolution: 9. Photosynthesis Ch. 10.1 through 10.3 10. Cell Cycle Ch. 12.1, 12.2 11. Meiosis Ch. 13.1 through 13.3 12. Mendelian Genetics Ch. 14.1 through 14.4 13. Chromosomes Ch. 15.1 through 15.4 14. DNA Ch. 16.1 through 16.3 15. Gene Expression Ch. 17.1 through 17.5 16. Gene Regulation Ch. 18.1 through 18.4 17. DNA Technology Ch. 20.1, 20.2, 20.4 18. Human Genetics Ch. 14.4, Ch. 15.4, 15.5 19. Darwinian Evolution Ch. 1.2, Ch. 22.1 through 22.3 20. Microevolution For ARC-103 Lectures with Dr. d'Arville: Review Session: Wednesday, November 5th - 6:40-8:00 pm, Hill 114, Busch For Hickman-138 Lectures with Dr. Bendaoud Review Session: Friday, November 7, 3:55 - 5:15 pm, Hickman 138, Douglass For Hickman-114 Lectures with Dr. Keating: Review Session: Wednesday, November 5, 10:20 - 11:40am, Lucy Stone Hall Auditorium (Livingston campus) Lecture 9: Photosynthesis (10.1-10.3) Concept 10.1 – photosynthesis converts light energy to the chemical energy of food Concept 10.2 – the light reactions convert solar energy to chemical energy of ATP and NADPH Concept 10.3 – the Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO to su2ar Overview: The Process that feeds the Biosphere - Photosynthesis is the process that converts solar energy into chemical energy o Photoautotrophs are the products of the biosphere, using sunlight to produce organic molecules from CO2 and other inorganic molecules o Almost all heterotrophs, including humans, depend on photoautotrophs for food and O2 Concept 10.1: In chloroplasts, photosynthesis converts light energy to the chemical energy of food (Fig 10.4) - CO2 enters and O2 exits the leaf through stomata in epidermal layer of leaf - Chloroplasts are found mainly in mesophyll cells, which sit between the outer and inner epidermal layers - Chloroplasts contain chlorophyll (in thylakoids- which are arranged in stacks called grana) - Chlorophyll captures light energy Fig 10.5: H2O is split into hydrogen and oxygen - Hydrogen electrons are incorporated into sugar molecules - Oxygen and water are released as by-products - Reactants: 6 CO2 + Photosynthesis is a Redox Reaction - Photosynthesis reverses the direction of electron flow compared to respiration o H2O is oxidized and CO2 is reduced - While respiration is exergonic, photosynthesis is endergonic; the energy boost is provided by light The Two Stages of Photosynthesis: A Preview - Fig 10.6 Light Reactions (photo part) and Calvin cycle (synthesis part) o The light reaction (in thylakoids) Splits H2O Releases O2 Reduces NAPD+ to NADPH Generates ATP from ADP = photophosphorylation o Dark reaction (the Calvin Cycle)(in stroma or fluid between grana) Forms sugar from CO2: carbon fixation Oxidizes NADPH to NAPD+ (+e-) Hydrolyzes ATP to ADP and P Concept 10.2 The light reactions convert solar energy to the chemical energy of ATP and NADPH Fig. 10.11 - Thylakoid membranes sit in stacks called grana; contain chlorophyll and enzymes - Chlorophyll a is the main photosynthetic pigment - Accessory pigments, such chlorophyll b, broaden the spectrum used for photosynthesis - Accessory pigment’s called carotenoids absorb excessive light that would damage chlorophyll When a pigment absorbs light (photon), it goes from a ground state to an excited state - Photons are given off = fluorescence (absorbs at one wavelength and emits at another) - Emitted light represents energy that can be captured by an acceptor (e.g. photosynthesis) o Chlorophyll b absorbs at about 450-500 nm and 600-650 (yellow green) o Chlorophyll a absorbs at 400-450 nm and 650-700 nm (blue green) The Photosystem sits in the Thylakoid Membrane (Fig 10.13) - In each photosystem: o Light harvesting pigment complexes composed of proteins, carotenoids and chlorophyll b help to enhance absorption of light )photons) o Transferring their energy to chlorophyll a in the reaction centers at the core of the photosystem There are two types of photosystems that sit in the thylakoid membrane (Fig 10.14) - Photosystem I (PS I) – which evolved first – is best at absorbing wavelengths of about 700 nm o The reaction-center containing chlorophyll a is called P700 - Photosystem Ii (PS II) is best at absorbing wavelengths of about 680 nm o The reaction center containing chlorophyll a is called P680 During light reactions, there are two possible routes for electron flow: cyclical and linear - Some organisms such as purple sulfur bacteria have PS I but not PS II o Cyclic electron flow is thought to have evolved before linear electron flow o Cyclic electron flow uses only photosystem I and produces ATP, but no NADPH No oxygen is released Cyclic electron flow generates surplus ATP FIG 10.12 Linear electron flow in plants is the primary pathway involving both photosystem I and II, producing ATP and NADPH that can be used in the Calvin cycle Photosystem II: P680+ is a strong oxidizing agent 1. A photon of light hits pigments complex boosting e- to a higher level a. Photon energy is passed among other pigment molecules until it excites the 2 electrons in P680 2. e- are transferred from P680 which becomes P680+ (oxidized) and an electron acceptor 3. H2O is split by enzymes: Two e-, 2H+ and an O atom are released a. e- are transferred to P680+ b. 2H+ released into thylakoid space c. O atom combines with another O atom from another process = O2 (biproduct) 4. Photoexcited e- from PS II are transferred to electron transport chain between PS II and PS I a. Membrane bound electron carriers (e,g, cytochrome) pass electrons from one carrier to next; each carrier is reduced, gaining energy 5. This energy is used to pump H+ into thylakoid space a. Contributes to proton (H+) gradient that drives chemiosmosis (production of ATP via ATP synthase) In PS I (like PS II), transferred light energy excites P700 - Meanwhile in PS II (P700) 6. A photon of light hits a pigment molecule; boosting e- to a higher level a. Photon energy is passed among other pigment molecules until it excites the 2e- in P700 b. Becomes P700+ (oxidized) and an e- acceptor - P700+ now accepts the electrons as they are passed down from PS II - Each electron “falls” down an electron transport chain from PS I to the protein ferredoxin (Fd) 7. Photoexcited e- are passed from PS I e- acceptor, to protein Fd 8. Two electrons are transferred from Fd to NADP+ via reductase producing NADPH a. NADP+ has the capacity to carry two electrons. NADP+ + 2e- Light Reaction Fig 10.18 The light reactions and chemiosmosis: the organization of the thylakoid membrane In Summary: the light-dependent reactions use solar power to generate ATP and NADPH, which provide chemical and reducing power, respectively, to the sugar-making reactions of the Calvin cycle. An incidental by-product of the light dependent reactions of oxygen A Comparison of Chemiosmosis in Chloroplasts and Mitochondria - Chloroplasts and mitochondria generate ATP by chemiosmosis, but use different sources of energy o Mitochondria transfer chemical energy from food to ATP o Chloroplasts transform light energy into the chemical energy of ATP - Spatial organization of chemiosmosis differs between chloroplasts and mitochondria but also shows similarities Fig 10.17 electron transport chains transform redox energy to a proton- motive force – potential force stored in H+ gradient across membrane - An electron transport chain pumps H+ ions to the inter-membrane space (M) or thylakoid space (C) - Drives ATP synthesis as H+ diffuse back into mitochondrial matrix (M) or stroma (C) Concept 10.3: The Calvin cycle uses chemical energy ATP and NADPH to reduce CO2 to sugar - Citric acid is catabolic, oxidizing acetyl CoA and using energy to synthesize ATP - Calvin cycle is anabolic, building process carbohydrates from smaller molecules and consuming energy o The Calvin cycle, like the citric acid cycle, regenerates its starting material after molecules enter and leave the cycle o Carbon enter in form of CO2 and leaves as sugar Using ATP as an energy source Calvin Cycle has three phases (carbon fixation, reduction, regeneration of CO2 acceptor) 1. Carbon enters the cycle as CO2, leaves as sugar named glyceraldehyde 3-phosphate (G3P) 2. For net synthesis of 1 G3P, cycle must take place three times, fixing three molecules of CO2 3. Light reactions sustain Calvin cycle by regenerating ATP and NADPH ……………………………………………….. ………………………………………………..………………………… Lecture 10: Cell Cycle (12.1 and 12.2) - Concept 12.1: Most cell division results in generally identical daughter cells - Concept 12.2: Mitotic phases alternate with interphase in the cell cycle - General: Cell Theory: Cells are basic living units of organization and function in all organisms all cells come from other cells —> life only comes from life Concept 12.1: Cell Division result in genetically identical daughter cells reproduction growth & development tissue renewal Some examples: o amoeba dividing into 2 cells (binary fission) o sand dollar: fertilized egg dividing forming 2 cells o divide bone stem cells give rise to new blood cells - Figure 12.3 & 12.4: Eukaryotic Chromosomes as cell approaches division, chromatin (DNA + chromatin) condenses and chromosomes become visible each diploid human cell has 46 chromosomes (3b base pairs) o made up of 23 pairs of chromosomes (22 pairs of autosomes; 23 pair looks different) o karyotype allows scientists to compare the two (similar or different) Number of chromosomes varies: wolf has 78, roundworm has 21 - Prokaryotes: one circular DS DNA molecules (re: mitochondria and chloroplasts) + plasmid o Plasmid: a genetic structure in a cell that can replicate independently of the chromosomes o typically a smaller circular DNA strand in the cytoplasm of a bacterium or protozoan. no chromosomes (rather binary fission) -The Gene chromosomes contain DNA, housing genes o informational units responsible for structure of all proteins in a cell o hundreds of thousands of genes on each chromosome o each gene located at particular locus (location/places) on a chromosome o genetic information arranged in linear sequence on chromosome o humans have about 20,000 genes telomere sequences at each end of chromosome o prevent the chromosomes from losing genes and fusing o like sneakers and lace - the plastic tip @ the end of the lace • chromatin = DNA + protein o Chromatin undergoes changes in pacing during the cell cycle (Figure 16.22) DNA = helix (double stranded molecule) - Watson & Crick Model o series of nucleotides = polymerization o as it starts to wind like a rope/cotton wheel the center = protein = octet of little proteins = histories o help to keep the structure o entire structure = nucleosome o remember that DNA + protein = chromatin once interphase is done —> moves to a more tightly wound configuration o scaffolding protein + linker protein (stabilize nucleosome) = compact Figure 12.5: Chromosome duplication and distribution during cell division o Centromeres link chromosomes together - help in separation made out of protein - Concept 12.2: Somatic Cells and Germ-line Cells Divide by Mitosis - Figure 12.6: Throughout embryogenesis, all diploid cells divide by mitosis then o all cells will continue to divide until specialization terminal differentiation = specialized = called G zero = G0 o terminally differentiated somatic cells enter G0 example: mature muscle, liver parenchyma, mature RBC’s, etc not destined to divide again o others remain as stem ells, moving through G1 to replace example: blood, skin (multiple layers) constantly divide when they need to o Germ-line cells divide by meiosis to become haploid Human cells have cycles o anywhere between 8 - 20 hours (the average is about 12 hours) o Interphase is about 11.5 hours, and M phase is about .5 hours - Figure 12.6: Interphase (example 11.5 hours) First Gap Phase (G1 : 5 hours) o prepare for S phase o synthesizes enzymes (etc) for DNA replication o mitochondria divide Synthesis Phase (S: 4.5 hours) o DNA replication produces sister chromatids o histone (H1 linker) and cyclins synthesized Second Gap Phase (G2: 2 hours) o RNA, protein synthesis continues o Centrosomes (+ centrioles) replicate Centrosome = vital in the process of mitotic spindle (used to separate chromosomes) - Figure 12.4: Interphase Chromosomes Duplicate During S Phase Each homologous chromosome becomes a pair of identical sister chromatids made up of chromatin (DNA + protein) Held together by a centromere region (via cohensins) Each sister also has kinetochere: multi protein complex (at centromere region) to which spindle microtubulers bind Know the difference between sisters and non sister (only combination of nonsisters) Random: The difference between mitosis and meiosis o Mitosis: cell division that results in two daughter cells each having the same number and kind of chromosomes as the part nucleus typical of ordinary tissue growth o Meiosis: cell division that results in four daughter cells each having half the number of the chromosomes of the parent cells production of gametes and plant spores M Phase (.5 hours in a 12 hour cycle) o Mitosis g2 ends = mitosis begins produces two nuclei identical to part Includes stages: prophase, pro-metaphase metaphase, anaphase, telophase (PPMAT) o Cytokinesis cytoplasm divides two daughter cells produced - Figure 12.8: During prophase, the Mitotic Spindle Forms each centrosome contains 2 centrioles (centrioles not in plant cells) embedded in y tubulin one end of a microtubule becomes stabilized in each centrosome the other end goes through dynamic instability; producing mitotic spindle o aster microtubules: sit and polymerizes; shooting stars out of centrosomes o kinetochore microtubules = connect to proteins = goes directly through the chromosome o interpolar microtubules = above and below (center the chromosomes = stabilization) - Microtubules tubulin heterodimers (alpha, beta) assemble into linear protafilaments at prophase, microtubules start to polymerize out of the centromeres microtubules grow and shrink during growth, heterodimers are added to end of microtubule, and during shrinkage come off as intact subunits (dynamic instability) - Random Facts about image: once formed dimer does not break —> protofilament —> microtubule - Centrosome on either side of the cell = asters negative end locks onto centrosomes and stars building/polymerizes (dynamic instability to move backward and forward) —> until it hits a chromosome chromosome combines with microtubule = can bring chromosomes wherever it needs to be stabilize chromosomes in the center of the cell the one that goes directly through the centrosomes = kenetichore - Figure 12.7b: Prophase chromosomes become visible as long as chromatin fibers begin to condense producing compact mitotic chromosomes (via condensin) nuclear envelope begins to disappear mitotic spindle forms - Figure 12.7C: Prometaphase Nuclear envelope, nucleolus continue to fragment polymerizing spindle microtubules seek out chromosomes (dynamic instability) o kinetochore microtubules move toward chromosome and capture sister chromatids at kinetochores chromosomes are moved toward cell’s mid plane (+ to center of cell) o via motor protein (kinesin) motor proteins bring towards the center or away (like the man walking with a log on it’s back) - Figure 12.7D: Metaphase Chromosome align at metaphase plate and three types of microtubules are now visible o Polar: overlap, act as a guide o Kinetochore: attached to each sister chromosome’s kinetochore o Aster: maintaining spindle pole - Figure 12.7E: Anaphase Sister chromatids are pulled apart o cohesins destroyed by enzyme called separase (remember enzyme = -ase) Kinetochore microtubules shorten/depolarize o pulling chromosomes towards the poles Spindle Elongates o polar microtubules slide past each other at mid plane o decreasing overlap, helping to pull poles apart - Figure 12.9: During anaphase chromosome is walked along microtubule as it depolymerizes at kinetochore end, releasing tubulin subunits Mark = area where fluorescence of microtubules is bleach out - Figure 12:7F: Telophase Chromosomes assembles at poles and uncoil o starts to decadence due to ionic shift o condensin breaks down Nuclear envelope re-forms around chromosomes spindle disappears nucleoli reorganize Cytokinesis begins o if not cytokinesis = multinucleate example: fungi, Hodgkin’s Lymphoma (Reedsternberg cells) - Cytokinesis (Figure 12.10) In animal cells: actomyosin contractile ring attaches to PM around midline o constriction provides two identical daughter cells In plant cells: Golgi produces vesicles containing cell plate materials o vesicles collect inside cell and deposit cell plate, which becomes cell wall o 2 daughter cells result each producing own plasma membrane and with own cell wall outside ……………………………………………….. ………………………………………………..………………………… Lecture 11: Meiosis (13.1-13.3) Variations on a Theme Heredity: transmission of traits from one generation to the next = inheritance Variation: differences between individuals (child to parent and siblings) Genetics: study of heredity and variation Gametes: reproductive cells that transmit genes from one generation to the next Type of Reproduction Asexual reproduction Sexual reproduction o Comparing asexual and sexual reproduction Asexual Reproduction Single parent produces offspring o Single-celled organisms – split o Multi-cellular organism – bud or fragment Offspring are results of mitotic division o 1 diploid (2n) parent 2 diploid offspring o 1 haploid (n) parent 2 haploid offspring Clones are produced: offspring are exact copies of each other and of parent Advantages: o Generally rapid o Avoid time and energy to find mate o Produce lots of progeny (well adapted to environment) Sexual Reproduction Union of 2 gametes (sex cells) to form a zygote o Gamete (n) + gamete (n) zygote (2n) = fertilization o Gametes usually from different parents (egg and sperm) Gametes are result of meiotic division o Each diploid (2n) parents 4 haploid (n) cells (half the # of X 1 diploid offspring Offspring not genetically identical to parents (not clonal) Advantages: o Genetic variation o Some may be better able to survive environmental (change or stress) Description Chromosomes (Xs) in Humans Human somatic cells have 23 pairs of chromosomes Karyotype: ordered display of X Done during mitosis X highly condensed stained so that visible Homologous Chromosomes (X) Homologous X (homologs): pair of X Have same o Length o Centromere position o Staining pattern Carry genes controlling same inherited characters o Ex: if hair color gene is on one chromosome, then in other chromosome o In that pair will have a version of hair color gene at equivalent locus Number & Types of Chromosomes (X) Somatic cells: diploid (2n) 46 chromosomes 23 pairs of homologs o 1 pair of sex chromosomes Females: X & X Males: X & Y o 22 pairs: autosomes: remaining X’s Gametes: haploid cells (n) 23 chromosomes 1 set of chromosomes o 1 sex chromosomes In an unfertilized egg (ovum) X In a sperm cell X or Y o 22 autosomes: remaining Xs Replicated Chromosomes 2 identical sister chromatids Figure 13.4 Comparing the Sexual Life Cycles of Different Organisms A. Life cycle a. Generation to generation sequence of stages b. From conception to production of own offspring B. Fertilization and meiosis a. In all organisms reproducing sexually b. Maintains constant # Xs in each specie from one generation to next c. Alternate during life cycle d. Timing of 2 events varies among species The Human Life Cycle 1. Fertilization = fusion of haploid sperm from father with haploid egg from momther 2. Zygote = fertilized egg diploid 3. Mitosis: occurs during development from zygote to multicellular organism all somatic cells = 2 sets X 4. Meiosis: at puberty form gametes 2 sets to 1 set 5. Gametes: not produced by mitosis a. Develop from germ cells in ovaries and testes b. Egg and sperm are haploid Counter balances the doubling that occurs in fertilization The Human Life Cycle Figure 13.5? Variety of Sexual Life Cycles Figure 13.4? Humans and Most Other Animals Gametes – only haploid cells in animals No multicellular haploid stage Multicellular organism (2n) meiosis gametes (n) fertilization zygote mitosis multicellular organism (2n) Plants and Some Algae Alternation of generations. o Both a diploid and haploid multicellular stage o Sporophyte (2n) (multicellular diploid stage) meiosis makes spores (n) mitosis gametophyte (multicellular haploid stage) mitosis makes gametes (n) fertilization zygote (2n) mitosis sporophyte (2n) Fungi and Some Protists Only 1 diploid stage: single-celled zygote No multicellular diploid stage Zygote meiosis haploid cells mitosis haploid multicellular organism mitosis gametes fertilization zygote 4 Stages of Meiosis Like mitosis: replication of Xs before meiosis Two consecutive cell divisions: meiosis I and meiosis II Results in 4 daughter cells (not 2 like mitosis) Each ha half # of Xsl Stages: 1. Interphase 2. Meiosis I 3. Interkinesis 4. Meiosis II Interphase Same as in mitosis Xs duplicate _ centriole pairs replicate Each X now composed of 2 sister chromatids (exact copies) Sister chromatids held together by cohesins (proteins) Humans = 46 Xs = 92 chromatids Chromatin Meiosis I: Four Phases Prophase I (1: Synaptonemal Complex Form) Synapsis (“fastening together” homologous maternal & paternal Xs align and pair Synaptonemal complex forms: zipper-like structure holds homologous Xs together Resulting is a tetrad: 4 chromatids structure Prophase I (2: Crossing Over Occurs) Chromatin condenses Crossing over occurs between non-sister homologous chromatids enzymes break + rejoin DNA molecule new combination of genes genetic recombination important source of genetic variability Chiasmata: X-shaped crossover regions Prophase I: 3. Break down of: nuclear envelope and nucleolus 4. Spindle forms: Microtubules attach to kinetochores One in each centromere End of prophase I in humans o 46 Xs o 23 tetrads o 92 chromatids Metaphase I 1. Tetrads align on metaphase plate 2. Homologous Xs oriented to opposite poles 3. Kinetochores of X are attached to spindle a. Both sister kinetochores of one X attached to spindle of same pole b. Kinetochores of homologous X attached to opposite pole Anaphase I Disjunction: homologous Xs separate Sister chromatids o Still attached at centromeres o Move as single unit to same pole Chromosomes act independently Nondisjunction: 1 or + homologous Xs fail to separate go to same pole error Telophase I & Cytokinesis Beginning Telophase I o Xs partially decondense o Nuclear envelopes reorganize at each pole End of telophase I in humans o # Xs in each nuclei: 23 o # chromatids: 46 o # tetrads: 0 Cytokinesis occurs simultaneously, forming 2 haploid daughter cells o In animal cells cleavage furrow o In plant cells cell plate Prophase II Fast because Xs still partially condensed Spindle apparatus reforms No homologous Xs so no pairing Metaphase II Xs (each 2 chromatids) line up on metaphase Similar to metaphase of mitosis Sister chromatids not genetically identical (crossing over) Sister centromeres oriented to opposite poles Anaphase II Chromatids separate go to opposite pole Each now is a X Nondisjunction can potentially occur Telophase II and Cytokinesis Xs decondense Nuclear envelope reforms Cytokinesis: forms 4 haploids cells genetically distinct from one another & from parent cell End of meiosis in humans, each gamete has 23 chromosomes ……………………………………………….. ………………………………………………..………………………… Lecture 12: Mendelian Genetics (14.1-14.4) 1. Mendel and the Scientific Approach o Mendel discovered basic principles of heredity by breeding garden peas which had certain advantages Many varieties with distinct heritable characters (i.e flower color) Distinct character traits or variants of that property (i.e purple or white flowers) Mating could be controlled Each flower contained male (stamen) and female (carpel) organs Self pollination and crosspollination (fertilization between different plants) was easy o Mendel chose to track characteristics that occurred in two distinct alternative forms i.e White and purple flowers So Mendel used carieties that were truebreeding (plants producing offspring of same variety when they selfpollinate) AA x AA We know from this that individuals of each generation P, F1, F2 are the same o Mendel crossed contrasting, truebreeding white and purple flowered pea plants Mendel crossed true breeding white and purple flowers All F1 hybrids were purpleflowered When mndel crossed F1 hybrids, many F2 plants had purple flowers, but some had white Mendel discovered a 3:1 ratio of purple to white flowers, in F2 generation Purple was seemingly more dominant o Dominant vs Recessive traits Mendel reasoned that only the purple flower factor was affecting flower color in the F1 hybrids Mendel called the purple flower color a dominant trait (P) and the white flower color a recessive trait (p) The factor for white flowers was not diluted or destroyed because it reappeared in the F2 generation What Mendel called a heritable "factor" is now known as a "gene" Mendel observed the same pattern of inheritance in six other pea plant characteristics, each represented by two traits F2 = 3:1 He developed a hypothesis based on his observations 2. First: alternative versions of genes account for variations in inherited characters o Gene for flower color in pea plants exists in two versions (alleles), one for purple, the other for white flowers Each allele resides at a specific locus on a specific chromosome Allele (P) for purple flowers, DNA produces enzyme that helps synthesize purple pigment Allele (p) for white flowers, DNA doesn’t synthesize enzyme or purple pigment (white/no color) 3. Second: for each character, an organism inherits two allels, one from each parents o Mendel made this deduction without knowing abou the role of homologous chromosomes The two alleles at a partiular homolog locus may be identical i.e truebreeding plants of Mendel's P generation (PP, pp) 4. Third: If the two alleles at a locus differ: then o One (dominant allele) determines the organism's appearance (i.e P and purple) o And the other (recessive allele) has no noticeable effect on appearance o In the flowercolor example, the F1 plants had purple flowers because the allele for that trait is dominant, however they were about to pass the p gene to the next generation, bringing forth some white flowers in the F2 generation 5. Fourth: two alleles for a heritable character separate (segregate) during gamete formation and end up in different gametes o Egg or sperm get only on of two alleles present in organism o This segregation of alleles corresponds to the distribution of homologous chromosomes into different gametes in meiosis o There ae no rules about how each pair of homologs align on the metaphase plate o Therefore endel's Law of Segregation states that allele pairs separate during gamete formation, and "randomly" unite at fertilization 6. Each pair of homologs (DNA replicated) aligns randomly at the metaphase 1 and 2 plates 7. Mendel's segregation model accounts for the 3:1 ratio observed in the F2 generation o Alleles of each gamete's homolog randomly unite at fertilization o Possible combinations of sperm and egg can be shown using a Punnet square o Predicts random combination of alleles in F2 generation by listing all possible gametes from one parent with all possible from other parent 8. Genetic Vocabulary Use o An organism with two identical alleles for a character is said to be homozygous for the gene controlling that character Homozygous dominant (two dominant alleles) Homozygous recessive (two recessive alleles) o An organism that has two different alleles for a gene is said to be heterozygous for the gene controlling that character o Unlike homozygotes, heterozygoes cannot be truebreeding (alleles are different) 9. Phenotype versus Genotype o Because of the different effects of dominant and recessive aleles, and organism's traits do not always reveal its genetic composition o Therefore, we distinguish between an organism's phenotype, or physical appearance, and its genotype or genetic makeup In the example of flower color in pea plants, PP and pp plants have the same phentotype (purple because purple is dominant) but different genotypes (because white is recessive and hidden in one of the plants) 10. How can we tell the genotype of an individual with the dominant phenotype? o Such an individual could be either homozygous dominant (PP) or heterozygous (Pp) o SO the answer is to carry out a testcross: Breeding the mystery individual (?) with a homozygous recessive individual (pp) o If any offspring display the recessive phenotype, the mystery parent must be heterozygous (Pp) or (pp) phenotype would be impossible 11. Mendel's Law of Segregation was derived by following a single characteristic Fig 14.7 o Identifying the unknown genotype from an organism with a gominant phenotype (PP or Pp) o The F1 offspring were monohybrids, the individuals heterozygous for one character o The cross between heterozygotes was/is called a monohybrid cross 12. Mendel identified his second law of inheritance by following two characters at the same time o Crossing two truebreeding parents differing in two character produces dihybrids in the F1 generation (i.e. heterozygous for both characters) o A Dihybrid cross, a cross between F1 dihybrids, can then determine whether two characters are transmitted to offspring as a package (i.e. together or independently) An example would be crossing yellowround seeds with greenwrinkled seeds 13. Do alleles for each characer assort into fametes dependently, or remain together? Fig 14.8 o Greenround seeds and yellowwrinkled seeds can only be produced if independent assortment occurs o Otherwise only yellow, round and green, wrinked would be posssible 14. Using a dihybrid cross, Mendel developed the law of independent assortment o The law of independent assortment states that each pair of alleles segregates independently of each other pair of alleles during gamete formation o Strictly speaking, this law applies only to genes on different, nonhomologous chromosomes or those far apart fo the same chromosome o Genes located near each other on the same chromosome tend to be inherited together: Not enough room for crossover 15. Crossing over during Meiosis I increases the # of different types of gamete possible o Different allele pairs separate independently during formation of 4 gametes And because genetic recombination occurs to cause "swooping" of alleles between nonsister chromatids at Prophase 1 Therefore, one individual can make many different types of gametes 16. Mendel's laws of segregation and independent assortment reflext the rules of probability o When tossing a coin, the outcome of one toss has no impact on the outcome of the next toss o In the same way the alleles of one gene (PP, pp, Pp) segregate into gametes independents of another gene's alleles 17. The multiplication rule predicts combined probabilities of independent events o Independent events means occurrence of one event will not affect probability that another event will occur at the same time (two tossed coins coming up heads) o Segregation in a heterozygous plant is like tossing a coin o In a monohybrid cross, the probability of a gamete receiving one or other allele is 1/2 ……………………………………………….. ………………………………………………..………………………… Lecture 13: Chromosomes (15.1 – 15.4) Concept 15.1: Mendelian inheritance has its physical basis in the behavior of chromosomes • Mitosis and meiosis were first described in the late 1800s • The chromosome theory of inheritance states: – Mendelian genes have specific loci (positions) on chromosomes – Chromosomes undergo segregation and independent assortment • The behavior of chromosomes during meiosis can account for Mendel’s laws of segregation and independent assortment Morgan’s Experimental Evidence: Scientific Inquiry • The first solid evidence associating a specific gene with a specific chromosome came from Thomas Hunt Morgan, an embryologist • Morgan’s experiments with fruit flies provided convincing evidence that chromosomes are the location of Mendel’s heritable factors Morgan’s Choice of Experimental Organism • Several characteristics make fruit flies a convenient organism for genetic studies – They produce many offspring – A generation can be bred every two weeks – They have only four pairs of chromosomes • Morgan noted wild type, or normal, phenotypes that were common in the fly populations • Traits alternative to the wild type are called mutant phenotypes Correlating Behavior of a Gene’s Alleles with Behavior of a Chromosome Pair • In one experiment, Morgan mated male flies with white eyes (mutant) with female flies with red eyes (wild type) – The F 1 generation all had red eyes – The F 2 generation showed the 3:1 red:white eye ratio, but only males had white eyes • Morgan determined that the white-eyed mutant allele must be located on the X chromosome • Morgan’s finding supported the chromosome theory of inheritance Concept 15.2: Sex-linked genes exhibit unique patterns of inheritance • In humans and some other animals, there is a chromosomal basis of sex determination The Chromosomal Basis of Sex • In humans and other mammals, there are two varieties of sex chromosomes: a larger X chromosome and a smaller Y chromosome • Only the ends of the Y chromosome have regions that are homologous with corresponding regions of the X chromosome • The SRY gene on the Y chromosome codes for a protein that directs the development of male anatomical features • Females are XX, and males are XY • Each ovum contains an X chromosome, while a sperm may contain either an X or a Y chromosome • Other animals have different methods of sex determination • A gene that is located on either sex chromosome is called a sex- linked gene • Genes on the Y chromosome are called Y-linked genes; there are few of these • Genes on the X chromosome are called X-linked genes Inheritance of X-Linked Genes • X chromosomes have genes for many characters unrelated to sex, whereas the Y chromosome mainly encodes genes related to sex determination • X-linked genes follow specific patterns of inheritance • For a recessive X-linked trait to be expressed • A female needs two copies of the allele (homozygous) • A male needs only one copy of the allele (hemizygous) • X-linked recessive disorders are much more common in males than in females • Some disorders caused by recessive alleles on the X chromosome in humans • Color blindness (mostly X-linked) • Duchenne muscular dystrophy • Hemophilia X Inactivation in Female Mammals • In mammalian females, one of the two X chromosomes in each cell is randomly inactivated during embryonic development • The inactive X condenses into a Barr body • If a female is heterozygous for a particular gene located on the X chromosome, she will be a mosaic for that character Concept 15.3: Linked genes tend to be inherited together because they are located near each other on the same chromosome • Each chromosome has hundreds or thousands of genes (except the Y chromosome) • Genes located on the same chromosome that tend to be inherited together are called linked genes How Linkage Affects Inheritance • Morgan did other experiments with fruit flies to see how linkage affects inheritance of two characters • Morgan crossed flies that differed in traits of body color and wing size • Morgan found that body color and wing size are usually inherited together in specific combinations (parental phenotypes) • He noted that these genes do not assort independently, and reasoned that they were on the same chromosome • However, nonparental phenotypes were also produced • Understanding this result involves exploring genetic recombination, the production of offspring with combinations of traits differing from either parent Genetic Recombination and Linkage • The genetic findings of Mendel and Morgan relate to the chromosomal basis of recombination Recombination of Unlinked Genes: Independent Assortment of Chromosomes • Mendel observed that combinations of traits in some offspring differ from either parent • Offspring with a phenotype matching one of the parental phenotypes are called parental types • Offspring with nonparental phenotypes (new combinations of traits) are called recombinant types, or recombinants • A 50% frequency of recombination is observed for any two genes on different chromosomes New Combinations of Alleles: Variation for Normal Selection • Recombinant chromosomes bring alleles together in new combinations in gametes • Random fertilization increases even further the number of variant combinations that can be produced • This abundance of genetic variation is the raw material upon which natural selection works Mapping the Distance Between Genes Using Recombination Data: Scientific Inquiry • Alfred Sturtevant, one of Morgan’s students, constructed a genetic map, an ordered list of the genetic loci along a particular chromosome Sturtevant predicted that the farther apart two genes are, the higher the probability that a crossover will occur between them and therefore the higher the recombination frequency • A linkage map is a genetic map of a chromosome based on recombination frequencies • Distances between genes can be expressed as map units; one map unit, or centimorgan, represents a 1% recombination frequency • Map units indicate relative distance and order, not precise locations of genes • Genes that are far apart on the same chromosome can have a recombination frequency near 50% • Such genes are physically linked, but genetically unlinked, and behave as if found on different chromosomes • Sturtevant used recombination frequencies to make linkage maps of fruit fly genes • Using methods like chromosomal banding, geneticists can develop cytogenetic maps of chromosomes • Cytogenetic maps indicate the positions of genes with respect to chromosomal features Concept 15.4: Alterations of chromosome number or structure cause some genetic disorders • Large-scale chromosomal alterations in humans and other mammals often lead to spontaneous abortions (miscarriages) or cause a variety of developmental disorders • Plants tolerate such genetic changes better than animals do Abnormal Chromosome Number • In nondisjunction, pairs of homologous chromosomes do not separate normally during meiosis • As a result, one gamete receives two of the same type of chromosome, and another gamete receives no copy • Aneuploidy results from the fertilization of gametes in which nondisjunction occurred • Offspring with this condition have an abnormal number of a particular chromosome • A monosomic zygote has only one copy of a particular chromosome • A trisomic zygote has three copies of a particular chromosome • Polyploidy is a condition in which an organism has more than two complete sets of chromosomes • Triploidy (3n) is three sets of chromosomes • Tetraploidy (4n) is four sets of chromosomes • Polyploidy is common in plants, but not animals • Polyploids are more normal in appearance than aneuploids Alterations of Chromosome Structure • Breakage of a chromosome can lead to four types of changes in chromosome structure – Deletion removes a chromosomal segment – Duplication repeats a segment – Inversion reverses orientation of a segment within a chromosome – Translocation moves a segment from one chromosome to another Human Disorders Due to Chromosomal Alterations • Alterations of chromosome number and structure are associated with some serious disorders • Some types of aneuploidy appear to upset the genetic balance less than others, resulting in individuals surviving to birth and beyond • These surviving individuals have a set of symptoms, or syndrome, characteristic of the type of aneuploidy Down Syndrome (Trisomy 21) • Down syndrome is an aneuploid condition that results from three copies of chromosome 21 • It affects about one out of every 700 children born in the United States • The frequency of Down syndrome increases with the age of the mother, a correlation that has not been explained Aneuploidy of Sex Chromosomes • Nondisjunction of sex chromosomes produces a variety of aneuploid conditions • Klinefelter syndrome is the result of an extra chromosome in a male, producing XXY individuals • Monosomy X, called Turner syndrome, produces X0 females, who are sterile; it is the only known viable monosomy in humans Disorders Caused by Structurally Altered Chromosomes • The syndrome cri du chat (“cry of the cat”), results from a specific deletion in chromosome 5 • A child born with this syndrome is mentally retarded and has a catlike cry; individuals usually die in infancy or early childhood • Certain cancers, including chronic myelogenous leukemia (CML), are caused by translocations of chromosomes Lecture 14: Chromosomes (16.1 – 16.3) Concept 16.1 DNA is the genetic material Concept 16.2 Many proteins work together in DNA replication and repair Concept 16.3 A chromosome consists of a DNA molecule packed together DNA is the genetic material o Frederick Griffith (1928) worked with two strains of a bacterium, one pathogenic (S) and one harmless ® Heat-killed remains of the pathogenic strain (S) + living cells of the harmless strain, resulted in: Living cells made pathogenic as a result of contact with the heat-killed remains And assimilation of DNA that coded for the capsule in the S strain Fig 16.2 Griffith called this transformation - change in genotype and phenotype due to assimilation of foreign DNA Evidence came from studies of viruses that infect bacteria o Alfred Hershey and Matha Chase perormed experiments showing that DNA is the genetic material of a phage known as T2 Succh viruses, called bacteriophages (or phages) are widely used in molecular genetics research (Fig16.3) Fig 16.5 Two findings became known as Chargaff's rules; this influenced Watson and Crick o The base composition of DNA varies between species o In any species the number of A and T bases are equal and the number of G and C bases are equal o In 1953, James Watson and Francis Crick introduced double helical model for structure of DNA Building a Structural Model of DNA: Scientific Inquiry o After DNA was accepted as genetic material, challed was to determine how structure accounted for its role in heredity Maurice Wilkins and Rosalind Franklin used technique called X-Ray crystallography to study molecular structure Fig 16.6 Franklin produced a picture of the DNA molecule using this technique Franklin's X -ray crystallographic images of DNA enabled Watson to deduce that DNA was helical o The X-Ray images enabled Watson to deduce the width of the helix and the spacing of the nitrogenous bases (Fig U) o Purine base + pyriidine base = Wilkins and Franklin's structure o The pattern in the image suggested that the DNA molecule was made up of two strands, forming a double helix Difference between DNA and RNA is in their sugars o Both polynucleotides Concept 16.2: Many proteins work together in DNA replication and repair o Fig 16.9 parent molecule unwinds. Since the two strands of DNA are complementary, each strand can act as a template for new strand replication Watson and Crick's semiconservative model of replication o Fig 16.10 predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or "conserved" from the parent molecule) and one newly made strand DNA replication begins at particular sites called origins of replication to form replication bubbles o Fig 16.12b A eurokaryotic chromosome may have hundreds or even thousands of origins of replication; a bacterial cell only has one o DNA strands separate at A:T where H bonds are easier to break. Replication proceeds in both directions from each origin, until the entire molecule is copied At end of replication bubble is a replication fork; Y-shaped region where new DNA strand elongates o Topoisomerase: corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands o Primase: makes a short piece of RNA called a primer o Helicase: enzyme that untwist the couble helix at the replication forks o SS Binding proteins: bind to, maintain and stabilize single stranded DNA o Primer: DNA polymerases can't add to a SS and only to 3' end o RNA Primer: Thereforeinitiated with short RNA primer providing 3' end o Initiator protein + helicase = starting point for strand break Fig 16.14 DNA polumerases catalyze elongation of new DNA at replication fork o Most DNA polymerases require a primer and a DNA template strand o Rate of elongation is ~500 nucleotides As each deoxy-ribonucleotide joins DNA strand, it loses two phosphate groups as a pyrophosphate o Eg. dATP supplies adenine to DNA o Similar to ATP of energy metabolism BUT dATP contains deoxyribose while ATP contains ribose Fig 16.15 DNA polymerases add nucleotides only to free 3' end of growing strand o Therefore new DNA strand can elongate Lecture 15: Gene Expression (17.1-17.5) Concept 17.1- Genes specify proteins via transcription and translation Concept 17.2- Transcription is the DNA-directed synthesis of RNA: a closer look ▯ Concept 17.3- Eukaryotic cells modify RNA after transcription ▯ Concept 17.4- Translation is the RNA- directed synthesis of a polypeptide: a closer look ▯ ▯ Concept 17.1 ▯ George Beadle and Edward Tatum exposed bread mold to X-rays, creating mutants unable to survive on minimal media Using crosses, identified 3 classes of arginine- deficient mutants, each lacking a different enzyme necessary for synthesizing arginine ▯ Developed one gene-one enzyme hypothesis States that each gene dictates production of a specific enzyme, later revised to “specific polypeptide” ▯ RNA is the bridge between genes and the proteins for which they code Transcription is the synthesis of RNA using information in DNA; produces messenger RNA(mRNA) Translation is the synthesis of a polypeptide, using information in the mRNA Ribosomes are the sites of translation o In prokaryotes, translation of mRNA can begin before transcription has finished o In eukaryotic cells, the nuclear envelope separates transcription from translation ▯ Eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA which is then released into cytoplasm for translation A primary transcript is the initial RNA transcript from any gene prior to processing (Fig 17.3) The central dogma is the concept that cells are governed by a cellular chain of command : DNARNAprotein ▯ How are instructions for assembling amino acids into proteins encoded into DNA? There are 20 amino acids, but only four nucleotide bases in DNA Flow of information from gene to protein is based on a triplet code (genetic code) Words of a gene are transcribed into complementary non- overlapping three-nucleotide words of mRNA These words are then translated into a chain of amino acids, forming a polypeptide Fig 17.4 During transcription, one DNA strand is template for sequence for complementary nucleotides in RNA transcript For any given gene, only one of 2 strands is transcribed Same strand is used as template every time gene is transcribed During translation, mRNA base triplets, called codons (e.g. in a reading frame UGG UUU GGC) are read in 5’ to 3’ direction Each codon specifies amino acid (one of 20) to be placed at corresponding position along polypeptide ▯ Fig 17.5 Genetic code is redundant (more than one codon may specify a particular amino acid) The genetic code is nearly universal, shared by the simplest bacteria to the most complex anmals But not ambiguous; no codon specifies more than one amino acid Of the 64 triplets, 61 code for amino acids 3 triplets are “stop “ signals to end translation One is the start codon, or can specify methionine ▯ Concept 17.2 RNA polymerase pries DNA strands apart and hooks together RNA nucleotides complementary to DNA template RNA synthesis follows same base-pairing rules as DNA, except uracil subsitutes for thymine DNA sequence where RNA polymerase attaches is called the promoter The stretch of DNA that is transcribed is called a transcription unit The three stages of transcription (fig 17.7) ▯ Fig 17.7 Promoters include transcriptional start point and determines which strand is transcribed Eukaryotic cell’s promoter’s TATA box (upstream of the start point) is crucial in forming initiation complex in eukaryotes Several transcription factors mediate binding of RNA polymerase II to DNA& correct positioning Other transcription factors+RNA polymerase II form a transcription initiation complex RNA polymerase II unwinds DNA helix RNA synthesis begins at start point ▯ Fig 17.9 As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time Eukaryotic transcription elongates ~40-50 nucleotides/sec Nucleotides are added to 3’ end of growing RNA molecule Removal of 2 phosphates from nucleotide provides energy (as in replication) Genes can be transcribed simultaneously by several RNA polymerases ▯ The mechanisms of transcription termination are different in bacteria and eukaryotes In bacteria, polymerase stops transcription at end of a terminator sequence: o Polymerase detaches, transcript is released o mRNA can be translated without further modification o transcription and translation take place in the cytosol In eukaryotes, RNA polymerase II transcribes a polyadenylation signal sequence (AAUAAA) after termination sequence: o RNA transcript (made in the nucleus) is released 10-35 nucleotides past this polyadenylation seuqnece o Pre mRNA must now be modified ▯ ▯ Concept 17.3 Enzymes in the eukaryotic nucleus modify pre-mRNA before the genetic messages are dispatched to the cytoplasm for translation (RNA processing) These modifications share several functions o Prepare a functional mRNA for translation o Facilitate export of mRNA to cytoplasm (poly A tail) o Protect mRNA from hydrolytic enzymes (via 5’ cap) o Help ribosomes attach to 5’ end of the transcript Each end of pre-mRNA molecule is modified in a particular way (Fig 17.10) 5’ end receives a 5’ cap; a modified form of a guanine nucleotide 3’ end gets poly A-tail (50-250 adenine nucleotides) In addition : most eukaryotes genes and their RNA transcripts have long noncoding stretches of nucleotides (introns) that lie between coding regions (exons) in the protein-coding segment 5’ UTR= an untranslated region that is also the leader sequence Rna splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence (Fig 17.11) introns are removed, exons are eventually expressed (translated into amino acid sequences) a single gene can code for several proteins: particular exons of a gene may be included within or excluded from the final, processed mRNA (alternative RNA splicing) ▯ RNA splicing is carried out by spliceosomes (fig 17.12) Spliceosomes consist of a variety of proteins and several nuclear ribonucleoproteins (snRNPs-ribozymes) that recognize the nucleotides of splice sites, precisely Complex binds to key sequences along intron Intron is cut out and degraded Spliceosome joins exons together Concept 17.4 Fig 17.14 A cell translates an mRNA message into protein with the help of transfer RNA (tRNA) tRNAs transfer amino acids to a growing polypeptide in ribosome Ribos
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