Bio Unit Test #2 - PDF

Bio unit test #2 →Lecture #9 ( Mitosis ): - When the cell is not dividing, chromatin (euchromatin and heterochromatin) exists as a mass of very long, thin fibres. - When a cell is ready to divide, the chromatin is tightly packaged and condensed to form chromosomes. -...

Bio unit test #2 →Lecture #9 ( Mitosis ): - When the cell is not dividing, chromatin (euchromatin and heterochromatin) exists as a mass of very long, thin fibres. - When a cell is ready to divide, the chromatin is tightly packaged and condensed to form chromosomes. - 46 chromosomes total, with 23 pair (chromosomes with exact numbers are homologous chromosomes, they have same gene at the same loci but different alleles ) - Allele: any of the alternative versions of a gene that may produce distinguishable differences in an individual's appearance or behaviour - Haploid cell : contains one set of chromosomes, 23 total ( in sperm or egg) - The “n” number is the number of chromosomes - In a haploid cell n=23 - Diploid cell: contains 2 sets of chromosomes, 46 total,two of each kind - In a diploid cell 2n=46 - Autosomes chromosomes from 1 to 22 (all homologous ) - Sex chromosomes is 23rd pair (female= homologous; male= not ) → Cell division in plants: - Same mitosis but with no centrioles - Difference only in cytokenisis, because cells don’t pinch in half And daiugther cells are separated by cell plate that forms at the center Cell divide for: Tissue renewal, growth and development and asexual reproduction  Cell cycle: 1. Interphase: - G1 phase: Growth period Extensive synthesis of new organelles When gene expression (transcription and translation ) takes place - S phase: DNA replication, meaning duplicating DNA molecule An exact copy of each chromosome is produced The two strands of the “parental” duplex separate at the replication fork and serve as template strands for the synthesis of the daughter strand. DNA polymerase: enzyme for making daughter strand of DNA (that grows from 5’ to 3’). It creates phosphodiester bonds between deoxyribonucleotides. DNA replication is semiconservative: because after replication, each new DNA duplex will consist of one strand that was originally present in the parental duplex and one newly synthesised “daughter” strand. Sister chromatids: copied chromosomes (contain same genetic info) and attached by centromeres Before S phase there’s 0 sister chromatids After S phase there’s 46 sister chromatids Chromosomes: Piece of DNA, same # = same gene different alleles Not same #= contain different gene Chromatids:At S Phase chromosomes are duplicated After S Phase each chromosomes is composed of two identical chromatids Sister chromatids: Two identical chromatids held together by a centromere - G2 phase: 2nd growth phase, cell increase in size Gene expression Centrosomes duplicate Spindle fibres (microtubules) form  2. Mitotic phase: - Prophase:.Chromatin compacts into chromosomes.Nucleus remains intact (but the nucleolus disintegrates).Duplicated centrosomes separate and move around the nucleus..Microtubule fibres extend between the centrosomes forming the mitotic spindle. - Prometaphase:.Nuclear membrane breaks down..Centrosomes are now positioned at opposite ends of the cell..Some microtubules attach to the kinetochores (the precise point on a centromere where the microtubule attaches) - Metaphase:.Chromosomes become aligned along the middle of the cell (metaphase plate)..For each chromosome, the kinetochores of the sister chromatids are attached to microtubules coming from opposite poles. - Anaphase:.Centromeres break and sister chromatids separate..Chromosomes pulled to opposite ends of the cell by microtubules.Cells elongate.At the end of anaphase, each pole of the cell has a complete set of chromosomes. - Telophase: One copy of each chromosome is present at the opposite ends of the cell. The chromatin fibers starts to loosen and become less coiled. Spindle fibers disappear. Nuclear membrane forms around chromosomes. Telophase marks the end of mitosis, even if cell division is not entirely complete. →Cytokinesis - Cytoplasm divides into two new daughter cells, - Cell pinches in the midline (cleave furrow) - 2 new daughter cells form with identical genetic info - Cells enter G1 of interphase and repeat the cycle G0 phase: - Not all cells in your body actively participate in the cell cycle, since not all tissues require rapid replenishing of cells. - Many cells pause in the cell cycle somewhere between M phase and S phase for periods ranging from days to more than a year. - This period is called G0 phase and is distinguished from G1 phase by the absence of preparations for S phase. - Although cells in G0 phase have exited the cell cycle, they are still active in other ways, performing specialized functions. - Cells that form the lens of the eye and neurons are perpetually in G0 phase and therefore are non-dividing cells. → Lecture 10 (meiosis): Asexual reproduction Sexual reproduction ( humas reproduce ) Offspring identical to parents Offspring NOT identicale to parents Mitosis Meisois Low genetic variation Increases genetic variation Somatic cell Gametes (sex cells) All cells Sperm and ovum Each cell has 46 chromosmes 23 chromosomes only After mitosis: After misoisi: - Two daughter cells - Four daughter cells - Diploid 2n - Haploid n - 46 chromosomes - 23 chromosomes Identical cells Meiosis is the sex cell cell division and produces cells that: - Have ½ the number of chromosomes found in the original parental cell - Are genetically different, this is to not create clones and create a genetically diverse society  1. Interphase (same as mitosis) 2. Meiosis 1: - Prophase 1 Nucleus and nuclear membrane disappear Chromatin condenses into chromosomes Centrosomes continue separating and moving to opposite poles Homologous pairs group and form tetrads Synapsis → homologous chromosomes held together by proteins (allows crossing over to occur (pairing of homologus chromosomes Crossing over →nonsister chromatids exchange genetic material with equivalent part of a chromatid from the other homologous chromosome, which leads to formation of recombinant chromatid that combines genes inherited from each parent. Results is chromosomes that have the same number of genes - Metaphase 1 Spindle fibers move tetrads to cell midline Tetrads line up at the metaphase plate Tetrads (homologous pairs) orient randomly/independently at the midline  - Anaphase 1 Homologous pairs separate but sister chromatids remain attached! Because the homologous pairs separate, each side of the cell only contains one set of chromosomes! - Telophase 1 Chromosomes drawn to opposite ends of the cell Chromatids still attached by centromeres Nuclear membrane surrounds chromosomes Nucleoli reappear Reduced from 2N to N at this point (forming daughter cells are haploid & genetically different) - Cytokinesis Each daughter cell has both copies of one of each homologous chromosome.  3. Meiosis 2 - Prophase 2 Nuclear membrane & nucleoli disappear Spindles attach to kinetochore Centrosomes separate - Metaphase 2 Attached chromatids line up on midline of cell (sister chromatids are not identical because of crossing over) - Anaphase 2 Centromeres break Chromosomes drawn to opposite ends of the cell - Telophase 2 and cytokinesis Chromosomes drawn to opposite ends of the cell Nuclear membrane and nucleoli form Through meiosis, each progenitor cell gave rise to 4 daughter cells Each daughter cell has one chromosome (haploid) rather than two present in the progenitor cell  Genetic variation: Meiosis results in new combinations of genes! Mutations are the original source of genetic diversity and can create different versions of genes called alleles Reshuffling of alleles during sexual reproduction produces new combinations of genes and increases genetic variation The behavior of chromosomes during meiosis and fertilization is responsible for most of the genetic variation that arises in each generation 1. Crossing over 2. Independent assortment of chromosomes 3. Random fertilization → Independent assortment: Homologous pairs of chromosomes orient randomly at metaphase I of meiosis Each pair of chromosomes sorts maternal and paternal homologues into daughter cells independently of the other pairs Possible number of combinations is 2n, where n is the ploidy ( how many sets of chromosomes in a cell)number → Random fertilization: Contributes to genetic diversity because any sperm can fuse with any ovum The fusion of two gametes produces a zygote with any of about 70 trillion diploid combinations! → Lecture 11: Mendelian inheritance Genotype: combination of alleles present for the characteristic in a particular organism, example PP, Pp, pp Phenotype: appearance of the characteristic, example purple , white Characters: An observable heritable feature that may vary among individuals (e.g., hair colour, flower colour) Traits: One of two or more detectable variants in a genetic character (e.g., blond hair colour, red hair colour, purple flower colour) Gene locus: Each gene occurs on a specific chromosome and is located at a specific site, that location is called the gene locus (plural loci) (same for everyone) Heredity: Genetics deals with the way biological characteristics are inherited.The transmission of traits from one generation to the next Blended inheritance: over many generations, a freely mating population will give rise to a uniform population of individuals, it fails to explain other phenomena of inheritance, such as traits reappearing after skipping a generation True breeding: parental, homozygous Mendel’s experiment: 1. Remove stamens from purple flower 2. Took pollen from white flower 3. Fertilized purple plant 4. Collected the seeds and planted them Results: F1 offspring had purple flower ONLY 1. F1 crossed all purple flower, F2 had 25% white , 3:1 ratio→ purple:white “ Monohybrid cross” is a genetic mix between two individuals who have opposite homozygous genotypes. Example: purple flower with white flower. Mendel derived the law of segregation by looking at a single character, therefore focuses on one trait. Dominant/ recessive allele “ Dihybrid cross” identified the law of independent assortment by focuses on two traits. 2 pairs of alleles, on non homologous chromosomes. Two separate genes Number of possible gamete combinations= 2 ^ number of heterozygous genes Mendel’s model: 1.Inherited characteristics are controlled by discrete chemical units (genes) 2.Each individual contains a pair of such heritable factors (alleles) for a particular gene (diploid) 3.Law of segregation: During the formation of gametes, this pair is separated (or segregated), so that only one member of the pair appears in any one gamete 4.At fertilization, the single allele in the sperm and the single allele in the egg are combined so that the new individual again has a pair of alleles for that trai → Lecture 12: chromosomal inheritance - Incomplete dominance: Heterozygous form is intermediate between that of the 2 homozygous forms. Phenotypic ratio= genotypic ratio - Codominance and multiple alleles: heterozygous simultaneously expresses phenotype of both homozygotes. IA IB codominant to each other and A B dominant to O.Because we are diploid humans can only have 2 alleles , thus ABO involves 3 alleles - Epistasis: Presence of certain alleles of one locus can prevent or mask the expression of alleles of a different locus and express its own phenotype instead. - Pleiotropy: single gene that can affect multiple phenotypes, multiple traits - Polygenic inheritance: Many genes interact to affect the expression of one trait. ITt is the inverse of pleiotropy - Sex- linked: sex-linked genes only found on X chromosomes.Characteristics controlled by 2 alleles in biological females but only 1 allele in biological males. Biological females can be carriers (heterozygous), biological males can’t. Biological males are hemizygous, single allele determines condition. Dosage compensation: mechanism that makes the 2 doses in the female and the single dose in the male equivalent. X-Inactivation: Inactivation is random during early embryo. Mitotic daughter cells have the same inactive X. All cells still have same genetic makeup - Polyploidy: a condition in which the cells of an organism have more than one pair of homologous chromosomes. 3n - Aneuploidy: abnormalities caused by the presence of a single extra chromosome or the absence of a chromosome  - Nondisjunction: Aneuploidies arise as a result of an abnormal meiotic division; chromosomes fail to separate = nondisjunction. Happens during Anaphase (I or II). Can cause down syndrome, an extra chromosome on gene 21 → Patterns of inheritance using a pedigree ( diagram of family history ) 1. Autosomal dominant: affected individuals will always be heterozygous. One affected parent. 2. Autosomal recessive: may skip generation, parents can be not affected. 3. Sex-linked: carried on the X chromosomes. Males mostly/ only affected Recessive: affected son but unaffected parent dominant : not the case → Lecture 13: origin of life - Evidence of early life comes from fossils of microorganisms that are 3.5B years old. Earth formed about 4.6B years ago, by condensing from a vast cloud of dust and rocks that surrounded the sun. - The first geological Eon is called the Hadean: the planet had just formed and was very hot due to volcanoes. - The atmosphere of the early earth may have been a reducing ( addition of electrons) atmosphere, in which organic molecules could have formed; thick with water vapor, nitrogen (N2) and its oxides, carbon dioxide (CO2), methane (CH4), ammonia (NH3), hydrogen(H2), and hydrogen sulfide. But no O2 present. The energy for this organic synthesis could have come from lightning and intense UV radiation Early life stages: ❖ Abiotic Synthesis of Organic molecules (monomers) #1: Extraterrestrial origin, organic molecules may have arrived from some other planet. ( cosmic dust carried organic material to earth) Abiogenesis, organic molecules may have evolved from abiotic matter, as associations among molecules became more and more complex. Miller-Urey experiment, key molecules of life could have formed in the early earth atmosphere ❖ Synthesis of Organic polymers #2: To create polymers, monomers have to dehydrate synthesis, meaning lose a water molecule. Perhaps first organic polymers were synthesized and accumulated on rock or clay surfaces. If conditions are hot and dry enough, the water molecule can be lost and monomers can join 1. Volcanic activity generated high temperatures to form proteins on early Earth. Waves/rain splash dilute solutions of organic monomers onto fresh lava or other hot rocks, polymers form and wash back into the  ocean. But the problem is that very high temperatures would cause OM to break down 2. Clay has caused polymers to form. Amino acids clay = RNA protein ❖ Formation of vesicles (protocells)#3: Amphipathic molecules can self-assemble into bilayer structures (hydrophilic regions on molecules face water, hydrophobic regions interior) If an amphipathic molecule stays in contact with water, stable spherical structures called liposomes ( first type of membrane to appear) form. ❖ The development of hereditary mechanism (nucleic acid); Self replicating RNA #4: RNA is the first genetic material. And could catalyze protein formation RNA molecules are flexible: single stranded and can assume a variety of shapes Ribozymes (RNA enzymes) can make copies of RNA. RNA could have provided the template for DNA, a more stable genetic material - The first prokaryotes: Stromatolites are rocklike structures composed of layers of bacteria and sediment (oldest fossil 3.5B) - Prokaryotes dominated from 3.5 to 2 BYA - Autotrophs producing all required compounds for life - Origin of Eukaryotic cells ( Endosymbiosis): Dawn of the Photoautotrophs Most atmospheric oxygen is of biological origin, from the process of photosynthesis. By about 2.7 billion years ago, O2 began accumulating in the atmosphere and rusting iron-rich terrestrial rocks. This “oxygen revolution” from 2.7 to 2.3 billion years ago caused extinction of many prokaryotic groups. Some groups survived and adapted using cellular respiration to harvest energy - Aerobic bacteria = protected from environment, mitochondria Origin of protists (single celled eukaryotes), that took place in cyanobacteria - Cyanobacteria benefited from well-regulated environment Protist began to rely on photosynthesis of cyanobacteria(chloroplasts) First eukaryotic photosynthesizers (algae) - Archaean host = received lots of energy → Evidence for endosymbiosis : ​ Mitochondria and chloroplasts have: - Their own circular DNA, like prokaryotes - Reproduce through binary fission, like prokaryotes - Ribosomes that resemble bacterial ribosomes, such that they are affected by antibiotics - Many genes that are shared with prokaryotes - Produce energy → lecture #14: Descent with modification Aristotle: species are fixed and unchanging life-forms could be arranged on a ladder or scale of increasing complexity Carolus linnaeus: founder of taxonomy ( branch of classifying organisms ) Created binomial format → Homo sapiens Georges Cuvier: created Paleontology, the study of fossils discovered extinctions, one layer to the next some species disappeared Charles Lyell: principle of uniformitarianism, stating that the mechanisms of change are constant over time ! influenced darwin ! Malthus: populations grew faster than their food supply; reproduction and food production Lamarck: first to propose evolution( organism change over time), using the principle of 1. Use and Disuse 2. Inheritance of acquired trait. Although ultimately incorrect, he did recognize that environment can influence organisms and give rise to evolution → Darwin: after his voyage, he observed various adaptations of plants and animals in diverse environments. Example, he compared animals on islands with the mainland, SHOWING distinct differences. ADAPTATION - Adaptation: inherited characteristics of organisms that enhance their survival and reproduction in a specific environment. → Natural selection: - occurs due to interactions between individuals and their environment but they do not evolve. - Act only on heritable traits (traits that are passed from organism to offspring) - The population contains individuals with the favourable trait Population = smallest group that can evolve Evolution has to be over successive generations HOW EVOLUTION WORK BY NATURAL SELECTION: 1. Species can produce more offspring than environment can support Population size increases exponentially 2. Environmental resources are limited Struggle for existence due to a higher number of individuals than the environment could support. This leads to competition for food, water and space that also leads to being killed by predators. 3. Members of a population vary extensively in their characteristics. No 2 individuals are exactly alike, variations are heritable 4. Differential reproductive success Individuals whose inherited traits give them a high probability of surviving and reproducing are likely to leave more offspring than other individuals. Fitness: The more surviving offspring an individual produces, the higher its fitness will be. Inclusive fitness: measured by the reproductive success of its kin (individuals who share high levels of genetic similarities). EVIDENCE FOR DARWIN’S THEORY 1. Natural selection in action More light moths than dark because they blended better and weren’t accessible to predators. 2. Homology( similarity from common ancestry) Vestigial organs that are useless because they were leftovers from ancestors, which ​indicate that the organism evolved from ancestors in which the organ was functional. Molecular: universal code that is evidence for a common ancestor 3. Analogous structures and convergent evolution  Analogous is when characters are similar, but are not derived from a common ancestor.Analogous features demonstrate that organisms with separate ancestors may adapt in similar ways to similar environments. Example, wings on birds, bats and insects. 4. Biogeography Species tend to be more closely related to other species from the same area than to other species that live in different areas. 5. Fossil record Forms consistent with other inferences about major descent → Lecture 15 : Microevolution Evolution occurs in populations and not individuals because individuals do not evolve Populations: all the individuals of the same species that live in a particular place at the same time - Genetic equilibrium : not evolving, no change in genotypic or allelic frequency. - Hardy- weinberg principle 1. Allele and genotype frequencies do not change from generation to generation (no evolution is occurring) in a population at genetic equilibrium. 2. Any population in which the distribution of alleles conforms to p2+2pq+q2 = 1 is at genetic equilibrium 3. Genetic equilibrium only occur if: no mutations Random mating Extremely large population size No migration, no gene flow No natural selection → So the factor that cause microevolution are the inverse of the genetic equilibrium DEVIATION FROM H-W PRINCIPLE: 1. Mutation: produces genetic variation A mutation is a change in the nucleotide sequence of an organism’s DNA. New genes and new alleles originate only by mutation 2. Non-random mating Does not change allele frequencies, only changes with whom they mate  Assortative mating Phenotypically similar individuals mate Increases proportion of homozygous individuals Disassortative mating Phenotypically different individuals mate Produces excess of heterozygotes 3. Genetic drift: Random shift Random evolutionary changes in a population Increase genetic differences among different populations Decreases genetic variation within a population Genetic drift: Bottleneck in a large population are drastically reduced by a disaster. The bottleneck effect occurs when the numbers of individuals Genetic drift: Founder Occurs when a few individuals become isolated from a larger population. → summary of effects of genetic drift: 1.Genetic drift is significant in small populations 2.Genetic drift can cause allele frequencies to change at random 3.Genetic drift can lead to a loss of genetic variation within populations 4.Genetic drift can cause harmful alleles to become fixed 4. Gene flow: gain or loss of alleles Consists of movement of alleles among populations Results from migration 5. Natural selection - Results in certain alleles (those that increase fitness) being passed to the next generation in greater proportions - Natural selection increases the frequencies of certain genotypes, fitting organisms to their environment over generations. - Natural Selection = Adaptive Evolution There are three modes of selection: Directional selection favours individuals at one end of the phenotypic range, favouring one extreme of phenotypic range Disruptive selection favours individuals at both extremes of the phenotypic range, favoring both extreme of phenotypic range Stabilizing selection favours intermediate variants and acts against extreme phenotypes, against both extreme and favours intermediate variants → Lecture 16: speciation and phylogenetics - Origin of species 1.The morphological species concept: Characterizes a species in terms of its body shape, size, and other structural features 2.The ecological species concept: Views a species in terms of its ecological niche 3.The phylogenetic species concept: trace phylogenetic history of organisms (comparing morphology & molecular sequences). - To be of the same species, they must be able to reproduce with each other Reproductive barriers Prezygotic barriers (5 types): block fertilization from occurring by: Impeding different species from attempting to mate Preventing the successful completion of mating Hindering fertilization if mating is successful 1. Habitat isolation: same area but encounter rarely 2. Temporal isolation: breed during different times 3. avioural isolation:different behaviors that are not recognized by members in another population 4. Mechanical isolation:matting attempted but morphological difference prevent it 5. Gametic isolation: Sperm of one species may not be able to fertilize the eggs of another species Postzygotic barriers (3 types): prevent the hybrid zygote from developing into a viable, fertile adult: Reduced hybrid viability Reduced hybrid fertility Hybrid breakdown 1. Reduced hybrid viability: 2. Reduced hybrid fertility:  3. Hybrid breakdown: Speciation Can occur due to.. 1. Allopatric speciation: geographic separation of populations restricts gene flow. 2. Sympatric speciation:occurs in geographically overlapping populations when biological factors, such as chromosomal changes and nonrandom mating reduce gene flow. The history of descent with branching is called phylogeny Homologous (Character state was present in the common ancestor of the two groups and retained over time.) traits lead to divergent evolution Analogous (Character state independently evolved in the two groups as an adaptation to similar environments) traits lead to convergent evolution 6. Atmospheric conditions of early earth, and how it made it possible for OM to form - A reducing atmosphere and Intense UV radiation, which is an advantage to photographs, which released oxygen and helped aerobic bacteria which then formed OM. 7. Ingredients a trait needs to have in order to be affected by natural selection - It needs to be heritable - It needs to be variable - Its diversity has to affect the survival rate of the trait holder 8. Biogeography? And how is it used as evidence of evolution - It means that species tend to be more closely related to other species from the same area than to other species that live in different areas. - Suggests a common ancestor adapts to various habitats. - This resulted in populations becoming isolated in different environments, à evolved differently. 1. What mendel's monohybrid cross and dihybrid cross were and what he deduced from each experiment - “ Monohybrid cross” is a genetic mix between two individuals who have opposite homozygous genotypes. Example: purple flower with white flower. Mendel derived the law of segregation by looking at a single character, therefore focusing on one trait. Dominant/ recessive allele - “ Dihybrid cross” involves studying two traits at the same time (e.g., seed shape and color) to observe how they were inherited. It identified the law of independent assortment by focusing on two traits. 2 pairs of alleles, on non homologous chromosomes. Two separate genes 2. Explain what is meant by a synapomorphy - Shared (two or more taxa have it ), derived trait (Most Recent Common Ancestor (MRCA) had it, its ancestor did not) - It helps identify which species branded off at what time and which species is more closely related to which species in comparison to others that are also similar. It even helps us identify the common ancestor. 3. Malthus - populations grew faster than their food supply; reproduction and food production - This led Malthus to infer that reproduction must eventually be checked by food production. - This idea significantly influenced Charles Darwin. Darwin applied Malthus's principle to the natural world, realizing that in nature, more organisms are born than can survive. This competition for limited resources means that only individuals with traits better suited to their environment are likely to survive and reproduce. Thus, Malthus’s insights provided Darwin with a foundation for his theory of **natural selection**, the mechanism by which evolution occurs.  Before S-phase After S-phase Diploid or haploid Diploid Diploid Sister chromatids 0 46 Chromatids (x2 SC) 0 46x2= 92 Chromosomes = two identical chromatids held by centromere ( sister chromatids)