Biology 102, Week 3 Notes
Biology 102, Week 3 Notes BIOL 102,
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This 9 page Class Notes was uploaded by Cambria Revsine on Sunday February 14, 2016. The Class Notes belongs to BIOL 102, at University of Pennsylvania taught by Dr. Sniegowski in Spring 2016. Since its upload, it has received 16 views. For similar materials see Biological Principles II in Biology at University of Pennsylvania.
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Date Created: 02/14/16
Biology 102—Week 3—Chapter 20, 2427, 3132 Lecture 7: Types of Mutation: Mutation is the ultimate source of evolutionary change Comparing genomes of closely related orgs. can show which genes were important enough to conserve so that mutations didn't become fixed, which did mutate Point mutation: one nucleotide changes to a different one o If it becomes fixed in a pop., called substitution Silent mutation: a substitution that doesn't change the AA, so phenotype stays the same o B/c most AAs match with more than one codon Nonsynonymous substitution: a substitution that does change the specified AA, or changes it to a “stop” Types of Gene Selection: If amino acid positions are under positive selection for change (there is a need for adaption, some AA sequences not as good as they could be), rate of nonsynonymous substitutions expected to be higher than synonymous natural selection favors some beneficial mutations If AA positions are under purifying selection (strong conservation of function, will not change), rate of of synonymous substitutions should be higher than nonsynonymous If AA replacements in the gene are neutral, two rates are expected to be similar (very rare) Genetic Variation among Humans: 6 billion base pairs per person (3 bill. from each parent) ~35 million differences from any other person, 10s of thousands of larger structure differences o A lot compared to other species Most differences are neutral, a few good, many bad (if we mate with others with it and children get homozygous recessive trait, would be very harmful; this is very rare) PostGenomic Age: Exponential growth in number of human genomes sequences over past 10 years As scientists get better at sequencing genomes, we know more what propensities to illnesses individuals have o Pros: early precaution to treat future diseases o Cons: know of future disease, health care providers might have access to people’s records History of Life: We know history of the formation of rock layers by looking at them bottomup Radioactive isotopes allow us to date rocks to a narrowish estimate o At first rocks are made up of pure isotopes, then decay to a different element Earth itself is 4.5 b.y.a. There has been way more than enough time since life arose ~3.8 x 10 years ago for 7 ~10,000,000 species, if each species forms every ~10 years o Many went extinct, either gradually or in a mass extinction Mass Extinctions: Not to scale, Precambrian was 8x longer than the rest Most extreme extinction was EndPermian one We might currently be in the 6 mass extinction There were many more extinctions than the mass ones Mass extinctions seem to occur at regular intervals Life originated 3.8 b.y.a., first eukaryotes 1.5 b.y.a. Cambrian explosion: rapid increase in the amount of oxygen in environment; rapid diversification of life Only at Cambrian in Paleozoic did most of the main groups of animals living today arise o Modern humans arose 200,000 y.a. Oxygen and Earth’s History: At first, little free2O Bacteria evolved ability to get H ions from H O 2n photosynthesis (~2.5 b.y.a.) Bacteria evolved ability to metabolize O 2~2 b.y.a.) o Beneficial in providing more energy to bacteria, so aerobes mostly replaced anaerobes o More complex cells evolved from more oxygen in the environment O 2especially increased in Carboniferous and Permian pds. From buildup of buried plant debris not oxidating Position of continents has changed over time influences sea level and global climate o Mass extinctions of marine animals when sea levels drop Mass extinctions also caused by meteorites o One 65 m.y.a. probably caused the endCretaceous extinction (dinosaur extinction) from debris and smoke that blocked the sunlight Lecture 8: Domains and Kingdoms: Categories have gone through much revision (old 5kingdom system) Threedomain system: present system with Bacteria (prokaryotes), Archaea (prokaryotes), Eukarya (eukaryotes) o Bacteria and Archaea probably have multiple kingdoms, not a definite number o Eukarya include Protista, Plantae, Fungi, Animalia o Carl Woese (19282012) used rRNA to discover Archaea rRNA good for comparison b/c it is ubiquitous, evolves slowly and lateral transfer is unlikely Archaea and Eukarya are more closely related to each other than to Bacteria, even though Archaea and Bacteria are both prokaryotes All the domains… Do glycolysis Replicate DNA semiconservatively DNA encodes peptides Produce proteins using essentially same genetic code Have plasma membranes and ribosomes Prokaryotes: More prokaryotes live in/on the human body than human cells, and more than all the people who have ever lived o Prokaryotes lining the gut are very helpful in aiding function Reproduce asexually by binary fission o But can sometimes transfer genetic info laterally Lack a cytoskeleton DNA is a single, circular molecule, not in a nucleus like eukaryotes Very few membraneenclosed organelles Most have a thick cell wall (different from plants’) o Bacterial cell walls have peptidoglycan, a sugar polymer) o Some Archaea have a similar molecule called pseudopeptidoglycan in their walls) Antibiotics interfere with synthesis of the cell wall, but are harmless to eukaryote cells Grampositive bacteria: have a dense cell wall made up of peptidoglycan outside of their plasma membrane Gramnegative bacteria: have a thin cell wall inside a double plasma membrane layer (periplasmic space in between membranewallmembrane Prokaryotes utilize many more metabolic pathways than eukaryotes o Most of the metabolic pathways in eukaryotes come from mitochondria/ chloroplasts (descended from bacteria) Anaerobes: Do not use oxygen as an electron acceptor in respiration Obligate anaerobes will die in the presence of oxygen Aerotolerant anaerobes don't use oxygen, but are not damaged by it Facultative anaerobes can shift metabolism between aerobic and anaerobic, like fermentation Obligate aerobes can only survive in the presence of oxygen Energy and Carbon: Photoautotrophs: energy source light, carbon source CO 2 o All 3 domains (land plants, use light energy to carbon fix) Photoheterotrophs: energy source light, carbon source organic compounds o Some bacteria Chemolithotrophs: energy source inorganic substances, carbon source CO 2 o Some bacteria, many archaea (bacteria in deep sea vents oxidize H S2 use this energy to carbon fix) Chemoheterotrophs: energy source organic compounds, carbon source organic comps. o All 3 domains **Organic compounds= carbon compounds made from other organisms Eukaryotes: Arose as the environment was gaining much more oxygen Might have arose from the fusion of a bacterium and archaean? Gained: o A flexible cell surface o Cytoskeleton o Nuclear envelope o Digestive vacuoles o Organelles by endosymbiosis DNA of a prokaryote is attached to its plasma membrane; the nuclear envelope of eukaryotes may have evolved from the plasma membrane Infolding of the plasma membrane beginning of development of nucleus Mitochondria: When Earth was young, cyanobacteria produced O w2ich was poisonous to many orgs., which were anaerobic Phagocytic eukaryotes “ate” and instead of digesting, kept a proteobacterium became mitochrondia o Endosymbiosis Mitochondria at first detoxified 2 by turning it to water, then became ATP producers Human respiratory system serves purpose of providing O to mitochondria 2 Lecture 9 Chloroplasts: Also derived from endosymbiosis o Evidence from nucleic acid sequencing and electron microscopy Three kinds of chloroplasts: Primary endosymbiosis: eukaryotic cell engulfs a cyanobacterium (gramnegative with inner and outer membrane) The chloroplasts in green algae, red algae, and land plants Modern red algae retain some of the peptidoglycan and pigments from the original cyanpbacteria Secondary endosymbiosis: eukaryotic cell engulfs another eukaryote with a chloroplast extra membrane around chloroplasts The chloroplasts in most photosynthetic eukaryotes beside green algae, red algae and land plants Present day euglenoids Tertiary endosymbiosis Prokaryote to Eukaryote: Hard cell wall became membrane Membrane infolding, folded around DNA Nucleus formed, ribosomes formed along infolding Flagellum added Endosymbiosis Protists: Eukaryotes that are not paraxoans, metazoans or fungi o The “leftovers” Not monophyletic, extremely diverse Some more closely related to animals and fungi, some more to plants Most are singlecelled but some are huge (kelp) Eukarya: Most of these divergences happened so long ago that there is no fossil record of it **Eukarya are more closely related to Archaea than either are to bacteria Animals: (Metazoa) Eukaryotes that develop from a single cell to many cells Heterotrophs Internal digestion (unlike Fungi; even though we technically digest outside b/c our bodies are “donuts”) No cell walls (unlike Fungi) Cells linked with gellike collagen and have intercellular junctions Most can’t move Often have specialized muscle tissues and nervous systems Animals have broadly similar organization and function of Hox genes, other developmental genes Monophyletic o The common ancestor was a flagellated protist related to choanoflagellates Evolution from protist to early “animal” Animal Groupings: First split between Parazoans sponges (no true tissue) and Eumetazoans (tissue) o Eumetazoans split between diploblastic (2 tissue layers: endoderm and ectoderm, radial symmentry) and triploblastic (3 tissue layers: endoderm, mesoderms, and ectoderm, bilateral symmetry, cephalization: head and brain at anterior end) Tripoblastic splits to Protostomes and Deuterostomes Animals have similar numbers of genes Have highly conserved genes and novel genes, as all organisms Hox Genes: Regulatory genes that conserve the homeobox sequence Produce Hox proteins o Hox proteins are transcription factors that bind to specific nucleotide sequences to turn on or off genes Located in gene clusters Head and tail end to Hox expression, corresponds generally to their gene location Present in Eumetazoans, not in sponges Number of clusters of Hox genes an animal has corresponds with its complexity **In animals, eyes of vertebrates and arthropods are an example of convergent structures, but genes of eye development are homologous Body Plan of Animals: Symmetry o Radial or bilateral (bilaterians) Body cavities: for cushioning organs, providing a skeletonlike structure, allowing external layer of muscles to move independently of gut and organs, and providing space to store eggs and waste o Acoelomates: lack a fluidfilled body cavity, movement by cilia o Pseudocoelomates: have a fluidfilled body cavity where organs are suspended, but not lined with mesoderm mesoderm only on the outside wall o Coelomates: true coelom lined with type of mesoderm called peritonium Segmentation External appendages Development of nervous system How do animals get their food? Sessile: animals stay in one place and move food to themselves Motile: animals move from place to place Filter feeders: use straining devices to filter small organisms and organic molecules from air to water Herbivores: adaptations for eating plants, symbiosis with microbes, herbivoreplant evolutionary race Predators: adaptations to kill and eat other animals, preditorprey evolutionary race o Omnivores: eat both plants and animals, often depending on life stage Parasites: live in or on another animal, mechanisms to overcome host defenses, usually don't kill hosts o Endoparasites (flatworms) o Ectoparasites (fleas and ticks) Detritivores: decomposers Cleavage: first division of a zygote Spiral: usually in protostomes o Mouth develops from blastopore o Determinate—each section is set to become a certain cell Radial: usually in deuterostomes o Anus develops from blastopore o Indeterminate—cell function is not fixed at first, if one part breaks off, can become a twin
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