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BI102 Exam 1
| Term | Definition |
|---|---|
| Changing life on a changing Earth | -Geological events that alter environments change biological evo ex. Isolation of orgs during lake form & Continental drift splitting up land masses -Life changes the planet it inhabits ex. evolution of photosynthetic orgs + evo of Homo sapiens |
| Changing life on a changing Earth | -Geo&biological history r episodic Only fundamental shifts that open new ways of life marked -Study of past events depend on preservation of data Fossil record less complete the further you go back Today orgs carry history in molec,metabolism,anatomy |
| Origin of Life | Earth and solar system formed 4.6 billion years ago Earth started as a ball of lava w/ no life As it cooled, a crust formed |
| Origin of Life | Early Earth, way diff atmosphere (strongly reducing, water vapor, similar chems to a volcanic eruption) Life unlikely during first few hundred million years (no liquid H2O) Oceans formed by condesation of H2O vapor as Earth cooled |
| Origin of Life | First life appeared bacteria-like 3.5-3.9 billion years ago 2 more billion years b4 eu c appeared Possible first c prod by chem/phy processes on early Earth |
| Four main stages in processes of early Earth | 1) Abiotic synthesis of small organic molec (monomers) 2) Monomers joined into polymers 3) Packaging of organic molec into protocells 4) Origin of self-replicating molec) |
| Abiotic synthesis of monomers | 1920s, Oparin and Haldane early Earth conditions favored synthesis of organic compounds from inorganic precursors (reducing conditions and no O2 atmosphere) requires nrg input (lightning, volcanic heat, UV) Oceans=primitive soup |
| Primordial soup | Hypothetical mixture in earth's early oceans, believed to be the chemical "broth" from which the first simple life forms emerged |
| Miller-Urey (1953) | Tested Oparin/Haldane Hypothesis with early earth atmosphere Water -> Water vapor -> electrode -> condensed Organic molecules found in sample |
| Abiotic synthesis of monomers | Existence of such atmosphere on early Earth is now thought unlikely, First organic comps synthesized near submerged volcanoes and deep-sea vents |
| Monomers joined into polymers | - Abiotic origin hypothesis formation of polymers from monomers in absence of enzymes / other cellular machinery -Experimental polymerization of organic molecules concentration on hot sand, clay, or rock maybe analogous to deep-sea vent, or lava |
| Packaging into protocells | Life defined by replication&metabolism Both props depend on RNA&DNA (unlikely in prim soup)->conditions for nuc development as proton Aggregates abiotically prod molec surr by lipid membr Exhibits props associated w/life- repro, meta, super8 intern env |
| Origin of self-replicating molec | RNA prob first genetic material (more than just genetic messenger for protein syn, some have enzymatic activity - ribozymes) |
| RNA ribozymes | catalyze numerous rxcs Self splicing Make complementary copies of short stretches of their own sequence or other short pieces of RNA - RNA sequences can evolve - 3D conformations |
| Origin of self-replicating molec | Early protoc w/self-rep catalytic RNA efficient @using resources Mutations in rep, basis for formation of novel molec Replace RNA w/DNA as carrier of genetic info(more stable) Lipid bilayer membr around fx strands of self-rep nuc A Primitive prok c |
| Why it's hard for a fossil to form | Few individuals have fossilized, even fewer have been discovered Biases species that have; existed for a long time, were abundant and widespread, and had hard parts |
| How rocks and fossils are dated | Sedimentary strata- reveals the relative ages of fossils (old, older, oldest) Index fossils - similar fossils found in the same strata in different locations. Allow strata at one location to be correlated w/ strata at another location |
| Radiometric dating | How absolute ages of fossils are determined based on decay of radioactive isotopes; half lives (how long it takes for 50% of sample to decay) C14 - half life of 5730 Ratio of C14 : Total carbon or N14 |
| Hadean Eon | 4.6-4 BYA No life Formation of solar system and earth |
| Archaean Eon | 2.5 - 4 BYA Formation of prokaryotic cells |
| Proterozoic Eon | 2.5 bya - 542 mya First Eukaryotic cells and orgs Ends with Cambrian explosion - major adaptive radiation produces most phyla of orgs |
| Phanerozoic Eon | 542 mya to now Contains the Paleozoic, Mesozoic, and Cenozoic eras |
| Paleozoic Era | 542 - 251 mya Complex euk c Plants and animals (fish, some reptiles, land plants, amphibians) Ends with Permian extinction |
| Mesozoic Era | 251 - 65.5 mya Dinosaurs along with flowering plants Ends with Cretaceous extinction |
| Cenozoic Era | 65.5 mya to now Humans and other mammals Homo erectus 1.8 MYA (Homo sapiens 200,000 -> 150,000 y/a) |
| Permian Extinction | 251 MYA Claimed about 96% of marine animals and 8/27 orders of insects Hypothesized to have been caused by volcanic eruptions in Siberia Incr in CO2 and temp, slowing ocean currents and reducing O2 |
| Cretaceous Extinction | 65.5 MYA Doomed many marine and terrestrial orgs, notably dinosaurs Hypothesized to have been caused by the impact of a large meteor |
| Stromatolites | Oldest known fossils, 3.7 to 3.5 b/y old Rocklike structures Composed of many layers of bacteria and sediment Date back 3.5 billion years ago |
| Prokaryotes | -Dominated evolutionary history from 3.5 - 2 bya as Earth’s sole inhabitants -May have arisen from protoc that utilized “prim soup” molec Developed into autotrophs, followed by heterotrophs -Transformed biosphere -2 branches: bacteria and archaea |
| Origin of electron transport components | -Electron transport -Chemiosmotic generation of ATP common to all 3 domains (Archaea, Bacteria, Eukarya) suggests early origin proton pumps originally to expel H+ reverse pump -generate ATP |
| Origin of photosynthesis | -Early photosyn non-oxygenic -Oxygenic photosyn ~3.5 billion years ago -primarily in cyanobacteria -O2 gets prod in light rxcs |
| Origin of photosynthesis | -O2 accumulated in the atmosphere 2.7 bya -posed challenge for life: poison for many orgs -provided opportunity to gain abundant nrg from organic molec (via cell respir) -provided orgs an opportunity to exploit new ecosystems |
| The first Eukaryotes | Earliest fossils of eukaryotic cells: 2.1 billion years ago – Traces of cholesterol in rocks dating 2.7 bya. – Cholesterol is a membrane component of eukaryotic cells. |
| Endosymbiosis theory | Theory for how complex euk c formed –mitochondria and plastids: formerly small prokaryotes living within larger host cells • gained entry to the host cell as undigested prey or internal parasites – host and endosymbionts then become a single organism |
| Endosymbiotic theory | Supported by plastids&mitochondria having -Similarities in inner membr struct & fx -Replicate by a splitting process -Similar to binary fission -Both have own circular DNA -Possess own transcription&translation machinery -Have their own ribosomes |
| Endosymbiotic theory | Other eukaryotic characteristics likely produced by endosymbiosis – large genomes – complex cellular structures – movement machinery - flagella and cilia (controversial) |
| Multicellular eukaryotes | evolved several times in eukaryotes • once the first eukaryotes evolved, a great range of unicellular and multicellular forms evolved • common ancestor of multicellular eukaryotes ~1.2 billion years ago • oldest fossils of eukaryotes ~1.8 billion |
| Multicellular eukaryotes | Larger multic euk don't appear in the fossils until several hundred m/y 570 million y/o fossils, prob animal embryos Ice age 750-580 mya, Snowball Earth Life confined to deep-sea vents&hot springs 1st major diversification parallel to end of ice age |
| Multicellular eukaryotes | 1st multic euk colonies- groups of autonomously repli c Some cells of colony specialized for different functions already in prok world (ex/ heterocyst, N2 fixing c) – Specialization in eukaryotes carried much further… |
| Cambrian Explosion | During first 10 years of Cambrian period (535-525), which is in Paleozoic era of Phanerozoic eon, animal phyla life exploded (end of an ice age) 1st appearance of predators |
| Examples of animals that came about after Cambrian explosion | Echinoderms, Chordates, Brachiopods, Annelids, Molluses, Arthropods |
| Colonization of land: plants, fungi, animals | 500 mya Plant colonization 420 mya - wax coating, symbiosis w/ fungi Terrestrial animals - widespread + diverse arthropods (eg. spiders) tetrapods (land vertebrates- 365 mya) |
| Continental drift | 3x land masses of Earth formed supercontinent: 1.1 bill, 600 mill, 250 mya Earth's continents move slowly over underlying hot mantle Oceanic+continental plates collide/separ8/slide past e/o Interxcs b/w plates can cause mountains/islands/earthquakes |
| Plasmids | Some species of bacteria also have smaller rings of extrachromosomal DNA Encode antibiotic resistance, etc |
| Continental drift | result in important geological processes, e.g.: – earthquakes – spreading of crust (seafloor spreading) – formation of mountain ridges |
| Pangaea | -Late Paleozoic era (250 mya): landmasses joined interior: cold / dry (much extinction) oceans deepened (extinction) -Mesozoic era (180 mya): breakup of Pangaea separ8 “evolutionary arenas", explains biogeographic puzzles like marsupials vs eutherians |
| Consequences of continental drift | Breakup of Pangaea & massive volcanism in Siberia corresponded w/ Permian extinction Mass extinction can alter ecological communities, the niches available to orgs, and create adaptive radiation May take 5-100 m/y for diversity to recover |
| Adaptive radiation | The evolution of diversely adapted species from a common ancestor upon introduction to new environmental opportunities |
| Worldwide Adaptive Radiations | -Mammals underwent an adaptive radiation after the extinction of terrestrial dinosaurs, expansion in diversity and size -Other notable radiations include photosynthetic prokaryotes, large predators in the Cambrian, land plants, insects, and tetrapods |
| Changes in Rate and Timing (Heterochrony) | Effect of genes Heterochrony is an evolutionary change in the rate or timing of developmental events • It can have a significant impact on body shape ex. contrasting shapes of human and chimpanzee skulls is result of changes in growth rates |
| Changes in Spatial Pattern (Homeotic Genes) | Substantial evolutionary change can result from alterations in genes that control the placement and organization of body parts ex. Homeotic genes which determine where basic features like wings & legs will develop or how a flower’s parts are arranged. |
| Homeotic Genes | Determine where basic features like wings, legs or flower parts are arranged in an orgs Changes the spatial pattern in orgs Contains Hox genes |
| Hox genes | Class of homeotic genes that prov positional info during development If expressed in wrong loc8, body parts can be prod in wrong loc Evo of vertebrates from invert, associated w/alterations in Hox 2 duplications in vert, mayb responsible 4 new traits |
| The Evolution of Development | The tremendous increase in diversity during the Cambrian explosion is a puzzle Developmental genes may play an especially important role Changes in developmental genes can result in new morphological forms |
| Changes in Gene Regulation | Changes in the form of orgs may be caused by changes in regulation of developmental genes instead of change in their seq E.g. 3-spine sticklebacks have fewer spines than marine relatives Same Gene seq, but diff regulation of gene expression in 2 groups |
| Three-spine stickleback fish | Shows change in orgs may be caused by change in developmental genes rather than sequence 3-spine sticklebacks have fewer spines than their marine relatives Gene seq is the same, but regulation of gene expression is different in two groups |
| Eutherians | major group of mammals characterized by a long gestation period where the fetus develops inside the uterus, nourished by a complex placenta, leading to young that are relatively well-developed at birth |
| phylogeny | – evolutionary history of a species or group of related species – determined by 1. data from the fossil record – information about ancient organisms 2. homology a) morphological b) Molecular (DNA) |
| Linnaeus | Systema naturae – two-part format of the scientific name of an organism • genus / species: Homo sapiens – species: reproductively isolated • Hierarchical classification scheme – groups species in increasingly broad categories |
| Hierarchical levels of biological classification | Domain -> Kingdom -> Phylum -> Class -> Order -> Family ->Genius -> Species |
| systematics | study of relationship of organisms |
| taxonomy | – ordered division of organisms into categories – based on a set of characteristics used to assess similarities and differences |
| phylogeny | Grouping of organisms based on evolutionary relationships |
| Phylogenetic tree | Used to depict hypotheses about evolutionary relationship -Each branch point represents the divergence of two species • “Deeper” branch points represents progressively greater amounts of divergence |
| How to make phylogenies | Look for homology and analogy –In morphology (body form) –In DNA |
| Homology | similarity due to shared ancestry accessed in morphology and molecular makeup |
| Morphological homology | -Same bones in all tetrapods –Modified for various functions |
| Molecular homology | Comparison of DNA segments from diff organisms |
| Analogy | Similar due to convergent evolution not common ancestor |
| Convergent evolution | Occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in different evolutionary lineages |
| Homoplasies | Analogous structures or molecular sequences that evolved independently Ex. Bat wings are analogous to a bird's wings; diff structure but same function |
| Cladistics | Analysis of evolutionary relationships Study of how species can be grouped into clades |
| Biofilms | Community of microbes that stick to surfaces and e/o –surface-adhering colonies –channels to distribute nutrients to center |
| Shared ancestral character | homologous structure that predates the branching of a particular clade from other members of that clade Shared beyond the taxon eg. presence of backbone (in all vertebrates) |
| Shared derived character | Evolutionary novelty unique to a particular clade eg. presence of hair on mammals (not all vertebrates) Useful in establishing a phylogeny Status of ancestral vs derived depend on phylogenetic lvl, requires outgroup comparison |
| Outgroups | Basis of comparison, species/group closely related to the ingroup, but less closely related than species are to e/o Allows differentiation between shared derived and shared ancestral characters |
| Heterocysts | protected from O2 prod. by photosynthesis Specialized c that perform nitrogen fixation, converting atmospheric nitrogen into ammonia |
| Monophyletic/Clade | Valid clade Consists of the ancestor species and all its descendants |
| Paraphyletic | Not a valid clade; missing descendants Consists of an ancestral species and some, but not all, of the descendants |
| Polyphyletic | Not a valid clade; includes organisms from different ancestral lines Includes numerous types of organisms that lack a common ancestor |
| Internal and Genomic Organization (of Prokaryotes) | Usually lack complex compartmentalization No membrane-bound organelles Some have specialized, infolded membranes that perform metabolic function |
| Phylogram | Length of a branch reflects # of genetic changes in a particular DNA or RNA sequence in that lineage |
| Ultrametric trees | Branching pattern is the same as in a phylogram Branch lengths correspond to time |
| Maximum parsimony | The tree that requires the fewest evolutionary events to have occurred in the form of shared derived characters |
| Maximum likelihood | given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events |
| Gene duplication | One of the most important types of mutation in evolution Increases the number of genes in the genome Provides further opportunities for evolutionary changes |
| Orthologous genes | Genes found in a single copy in the genome Can diverge only once speciation has taken place We share much in common with other organisms |
| Paralogous genes | Result from gene duplication, so they are found in more than one copy in the genome Can diverge within the clade that carries them, often adding new functions e.g. olfactory receptor gene |
| Molecular clock | Standard for measuring absolute time of evo change Based on observation that some genes & other regions of genomes appear to evolve @ constant rates rRNA seq slow ; mtDNA quick # of nucleotide substitutions proportional to time since species branch pt |
| Neutral theory of molecular clock | Much evo change in genes & p has no effect on fitness; not influ by Nat selection Rate of molec change in these genes & p should be regular like a clock Not as smoothly as neutral theory predicts, depends on region of genome ex-mutation hot spots |
| Transduction | Viruses transfer genes between prokaryotes |
| Tree of life | Suggests that eukaryotes and archaea are more closely related to each other than to bacteria Largely on ribosomal RNA (rRNA) genes, as these have evolved slowly |
| Not so Simple Tree of All Life | There have been substantial interchanges of genes b/w orgs in diff domains -Horizontal gene transfer is the movement of genes from one genome to another -Horizontal gene transfer complicates efforts to build a tree of life |
| Prokaryotes | -Thrive almost everywhere, even in environments too acidic, salty, cold, or hot for most other organisms -Diverse adaptations - astonishing genetic diversity -Bacteria and Archaea |
| Nitrogen metabolism | Prok can metabolize Nitrogen fixation: convert atmospheric nitrogen to ammonia Cyanobacteria – aquatic ecosystems Rhizobium – terrestrial ecosystems Associated with plant roots in “root nodules” on plants in the pea family (legumes) |
| Morphology of prokaryotes | Variety of shape but 3 most common Cocci (spheres), bacilli (rods), and spirillum (spirals) Lyme disease is a spirillum bacteria |
| Metabolic cooperation | Allows prok to use environmental resources they couldn't use as individual c Photosynthetic cells and nitrogen-fixing cells (heterocysts) exchange metabolic prod Heterocysts protected from O2 prod. by photosynthesis Some prok contain biofilms |
| Cell wall | Maintains c shape, prov phys protection, prevents lysis in hypotonic environs Bacteria c wall made of peptidoglycan, (not archaea) Many antibiotics prevent c wall form; inhibit peptidoglycan cross linking, ineffective against human c Ex. penicillin |
| Lysis | Cell is in hypotonic solution, takes in too much water, and bursts Prevented by cell wall |
| Gram stain | Used to classify prokaryotes Procedure: -Stain with violet dye+iodine -Rinse with alcohol -Stain with red dye –Two groups based on staining pattern due to cell wall composition Gram-positive or Gram-negative |
| Gram-positive bacteria | have a cell wall with a large amount of peptidoglycan that traps the violet dye in the cytoplasm. The alcohol rinse does not remove the violet dye, which masks the added red dye. |
| Gram-negative bacteria | have less peptidoglycan, and it is located in a layer between the plasma membrane and an outer membrane. The violet dye is easily rinsed from the cytoplasm, and the cell appears pink or red after the red dye is added. |
| Capsule | Covers c wall of many prok Sticky layer of polysaccharide or protein Can provide some protection from the environment |
| Fimbriae and pili | Some prok contain Allow them to stick to substrate or other individuals in a colony Sex pili: facilitate transfer of DNA during conjugation |
| Flagella | Half of all prokaryotes: directional movement Most motile bacteria propel themselves by flagella Structurally and functionally different from eukaryotic flagella |
| Taxis (motility) | In heterogeneous environment, many bacteria exhibit taxis; Ability to move toward or away from certain stimuli Chemotaxis: change of movement in response to chemicals Important in colony formation |
| Prokaryotic genome | Ring of DNA No defined nucleus: not surrounded by a Often located in a nucleoid region Some bacteria have smaller rings of extrachromosomal DNA called plasmids, which encode for antibiotic resistance |
| Binary fission | How prok reproduce Scarcity of nutrients which slows their metabolic activity |
| Endospores | Cell replicates chromosome, then surrounds it w/ durable wall Can remain viable in harsh conditions for centuries Lack of nutrients, extreme temps, poisons, boiling water Autoclave (120°C) usually kills them Formed by many prok |
| Adaptation | rapid reproduction Mutation: major source of genetic variation Also horizontal gene transfer Conjugation: transfer of plasmid DNA |
| Gene recombination | Prok ways to combine genes b/w individuals Transformation -cell absorb & integrate fragments of DNA (plasmids) from their environment Conjugation - cell directly transfers genes to another cell Transduction - viruses transfer genes between prok |
| Transformation | a cell can absorb and integrate fragments of DNA (plasmids) from their environment This allows considerable genetic transfer between prokaryotes, even across species lines |
| Conjugation | One cell directly transfers genes to another cell |
Created by:
phillipchristopherr