Bio 2 Exam 1 Notes Upd. PDF

**Lecture 2** - [Myiasis] - Invasion of tissue by fly larvae (maggots) - Feeding on living/dead tissue - [Facultative Myiasis] - Maggots develop in foul-smelling wounds and ulcerations (especially wounds producing pus) - [Maggot Therapy] - Introduce live (disinfected) maggot...

**Lecture 2** - [Myiasis] - Invasion of tissue by fly larvae (maggots) - Feeding on living/dead tissue - [Facultative Myiasis] - Maggots develop in foul-smelling wounds and ulcerations (especially wounds producing pus) - [Maggot Therapy] - Introduce live (disinfected) maggots into non-healing wounds - Clean out necrotic tissue (debridement) [History of Earth] - Archaen → Proterozoic → Phanerozoic → Cenozoic - - Billions of years ago\.... - 13.8 (big bang) → 4.6 (start of solar system) → 4.55 (origin/age of Earth) → 4 (cooling of Earth/formation of crust and oceans) → 4 to 3.5 (origins of life) [What is life?] - DNA, cells, metabolism, adaptation, homeostasis, growth, reproduction and evolution - Metabolism - Absorption of nutrients - Excretion of wastes - Energy acquisition and transformation (ex. Krebs cycle) - Cellular synthesis - Reproduction - Growth: duplication of all cellular components - Division of discrete units (cells) - Evolution - Variation, reproduction, mutation - Mutation: mistakes in copying cell components [Origins of Life: Stages 1-4] 1. Organic molecules in nucleotides and amino acids produced prior to the existence of cells 2. Nucleotides and amino acids became polymerized to form DNA, RNA and proteins 3. Polymers became enclosed in membranes 4. Polymers enclosed in membranes acquired cellular properties [Stage 1: Origin of Organic Molecules] - Conditions on early Earth may have been more conducive to spontaneous formation of organic molecules → this formation is the prebiotic (primordial) soup - Several hypotheses on where and how organic molecules originated - Reducing Atmosphere Hypothesis - Extraterrestrial Hypothesis - Deep Sea Vent Hypothesis 1. *Reducing Atmosphere Hypothesis* - Miller-Urey's 1952 experiment: - Set up sterile anerobic atmospheric conditions + electrical discharge → spontaneous formation of simple organic molecules → amino acids, simple carbs and lipids 2. *Extraterrestrial Hypothesis* - Meteorites brought organic carbon to Earth → this carbon includes amino acids and nucleic acid bases 3. *Deep-sea Vent Hypothesis* - Biologically important molecules may have been formed in the temperature gradient between extremely hot vent water and cold ocean water [Stage 2: Organic Polymers] - Experimentally, prebiotic synthesis of polymers was thought impossible in aqueous solutions (bc. hydrolysis competes with polymerization) - However, experiments have shown formation of nucleic acid polymers and polypeptides on clay surfaces [Stage 3: Formation of Boundaries] - Formation of boundary that separated internal polymers for environment  - What are characteristics that make protobionts possible precursors to living cells? - Boundary separating internal contents from external environment - Polymers inside contained info and has enzymatic function - Capable of self-replication - Living cells may have evolved from... - Coacervates - Droplets formed spontaneously from association of charged molecules - Enzymes trapped inside could perform metabolic functions - Liposomes - Vesicles surround by lipid layer - Clay catalyzes formation of liposomes that grow and divide - Encloses RNA [Stage 4: RNA world] - Many scientists favor RNA as first macromolecule of protobionts - RNA has 3 functions - Ability to store info - Self-replication - Enzymatic function (ribosome) - Advantages of DNA/RNA protein world: - Information storage -- DNA would allow RNA to do other functions instead of informational → DNA is less likely to suffer mutations - Metabolism -- proteins have greater catalytic potential and efficiency and can perform other tasks → cytoskeleton, transport etc. - Origins of Life \| Summary 1. Formation/accumulation of organic molecules 2. Polymerization of nucleic acids & proteins 3. Formation of protobionts 4. Synthesis of cell components by ribozymes 5. Synthesis of proteins by DNA, RNA, & ribosomes 6. Replication of DNA **Lecture 3/4** [Fossils & Types of Rock:] - Sedimentary - Contains fossils - Piles up, forms layers, becomes rock - Igneous - Used to date rock layers - Contains radioactive isotopes (unstable and decay w/ time) -- half-life - Measures amount of given isotope + amount of decay product - Metamorphic - Volcanic [Small fossils:] A close-up of microscopic images Description automatically generated - Stromatolites fossilized biofilms [Modern stromatolites:] - Hamelin Pool Australia - New cyanobacteria stromatolites - Some are pillars up to 5 feet high - Take 1000s of years to grow [Introduction to Evolution] 1. Changes in living organisms a. Genetic changes b. Environmental changes: i. Climate/temp ii. Atmosphere iii. Land masses iv. Floods v. Glaciations vi. Volcanic eruptions vii. Meteoric impacts 2. They can: c. Allow for new types of organisms d. Responsible for many extinctions [Time Periods] 1. Archaean (3.8-2.5 bya) a. First and all cells: prokaryotic -- no nuclei i. Bacteria vs archaea similar but diff. metabolism/genetics b. Anaerobic (don't require oxygen) organisms (no access to free oxygen) c. Heterotrophs -- energy via consumption ii. Not preserved d. Autotrophs -- energy via production iii. evolved as supply of organic molecules became less iv. were preserved v. formed stromatolites microbial mats of layered structure of calcium carbonate 2. Proterozoic (2.5 bya -- 543 mya) e. Multicellular eukaryotes arise \~1.5 bya f. Possible origins: vi. Individuals form a colony vii. Single cells divide but stay stuck together viii. Consequence: complexity and specialization of cells g. Volvocine green algae display variations in the degree of multicellularity  h. Multicellular eukaryotes (cells with nucleus) arise 1.5 bya i. Milestone in life = eukaryotes include all multicellular organisms j. First animals. -- invertebrates k. Bilateral symmetry -- facilitates movement l. Modern eukaryotes à ix. DNA -- in nucleus, mitochondria and chloroplasts x. archaea and bacteria contribute to nuclear genome xi. endosymbiotic relationships give rise to eukaryotic cells 3. Phanerozoic Eon m. Diversification of invertebrates and colonization of land plants and animals 4. Cambrian (543 -- 490 mya) n. Warm & wet w/ no ice @ poles o. Cambrian explosion xii. Abrupt increase in diversity of animal species 1. Cause unknown shell evolution, atmospheric oxygen, "arms race"? xiii. All existing major types of marine invertebrates plus many others that no longer exist p. Burgess Shale: xiv. No major reorganizations of body plans despite new species first vertebrates 5. Ordovician (490 mya -- 443 mya) q. Diverse group of marine invertebrates (trilobites & brachiopods) r. Primitive land plants and arthropods first invade land s. Towards end, abrupt climate change (large glaciers) = mass extinction more that 60% of marine invertebrates go extinct 6. Silurian (443-417 mya) t. Coral reefs appeared u. Large colonization by terrestrial plants and animals v. Spider and centipedes w. Earliest vascular plants transport system for water and nutrients 7. Devonian (417-354 mya) -- Age of fish x. Ferns, horsetails and seed plants (gymnosperms) xv. Insects emerge y. Tetrapods amphibians emerge z. Near end, prolonged series of extinctions eliminate many marine species 8. Carboniferous (354-290 mya) a. Rich coal deposits formed b. Very large plants, trees, amphibians prevalent c. First flying insects d. Amniotic egg emerges egg protected by membrane e. Giant fern tree form of petrified wood 9. Permian (290-248 mya) f. Pangaea (formed via continental drift) g. Amphibians prevalent; reptiles became dominant h. First mammal-like reptiles appeared i. Largest known mass extinction (Great Dying/ Permian-Triassic Extinction) xvi. 90-95% of all marine species and large proportion of terrestrial species eliminated xvii. Caused by glaciations and/or volcanic eruptions 10. Triassic, Age of Dinosaurs (248-206 mya) j. Many reptiles k. First dinosaurs + first true mammals l. Gymnosperms (nonflowering plants) dominate land plants m. Volcanic eruptions led to global warming + mass extinctions near the end 11. Jurassic (206-144 mya) n. Gymnosperms still dominant o. Dinosaurs dominant land animals p. First known bird q. Mammals present but not prevalent 12. Cretaceous (144-65 mya) r. Dinosaurs still dominant on land s. Earliest flowering plants (angiosperms) t. Mass extinction at the end of period (Cretaceous Tertiary/ K-T extinction xviii. \~66 mya xix. Large meteorite hit regions (Yukatan) -- lifting massive amounts of debris xx. "impacting winter lasting" \~ 2 years xxi. Climate change cascade \~10,000 years 13. Tertiary, Age of Mammals (65-1/8 mya) u. Mammals that survived diversified rapidly v. Angiosperms become dominant land plant w. Hominoids evolved about 7 mya 14. Quaternary (1.8 mya to present) x. Periodic ice ages cover much of Europe and North America y. Certain hominids become more human-like z. Homo sapiens evolve 130,000 years ago SUMMARY: Geological time scale: delineated/separated by formation and extinctions of species (coincide with what?) - Archean = bacteria and Achaea - Proterozoic = eukaryotes - Phanerozoic: - Paleozoic = land colonized - Mesozoic = dinosaurs - Cenozoic = hominoids **Lecture 5** [Intro. To Evolution] a. Theory of Evolution b. Evidence of Evolutionary change [What is evolution?] - Heritable change in one or more characteristics of a population from one generation to the next [Conceptual Levels of Evolution] - Microevolution - Changes in allele frequencies in a population over time - Macroevolution - The formation of new species or groups of related species \*Population: all members of a species that live in same area; have same opportunity to interbreed \*Species: a group of related organisms that share a distinctive form \*Allele: one of two or more forms of the DNA sequence of a gene [What is a theory?] - Theory -- a comprehensive explanation for a large body of info - Hypothesis -- a question that is subject to testing (falsifiable) [Prior to Darwin - 1700^th^ century evolutionary thinkers] - Linnaeus - Classified nature with a nested hierarchy - Binomial nomenclature - Lamarck - Adaptation to new environments - Inheritance of acquired characteristics [History -- 1800s] - Charles Darwin (1809) - British naturalist - Influenced theory in geology, economics and voyage of the beagle [Darwin's influences \| Peers] - Geology - Uniformitarism hypothesis (time is required for reoccurring changes on Earth like erosion) - Slow geological processes lead to substantial change - Geology → importance for Darwin → earth was much older than 6,000 years - Economics - Population growth linked to resources - Economics → importance for Darwin → only a fraction of any population will survive and reproduce when resources are limited - HMS Beagle - Mission of trip → map the coastline of southern south America → Darwin's job was to record everything (weather, animals, people, fossils) [Importance for Darwin] - Observations about animals/plants collected along the trip - Struck by distinct traits of island species - Galapagos island finches' similarities and also noted different feeding strategies - Specialization in feeding to obtain specific foods that changed per islands [Formulation of Theory] - Mid 1840s → formulated theory - 1856 → began writing this book - 1858 → Alfred Wallace (competitor of theory) - Darwin's & Wallace's papers published together - 1859 -- Darwin's *The Origin of the Species* is published detailing his ideas with observational support [Book: Descent with Modification] Darwin's evolution based on: 1. Variation within a given species - Heritable traits - Genetic basis not yet known 2. Natural selection - More offspring produced than can survive - Competition for limited resources - Traits that favor reproductive success become more common in a population [Fossils] - Fossils = transitional forms linking earlier and later form - Fossils illuminate the steps leading to the evolution of tetrapod - Evolutionary changes can be demonstrated even w/ incomplete fossil record [Biogeography] - The study of the geographical distribution of extinct/living species - Isolated continents and island groups have evolved their own distinct plant/animal communities - Ex: south California has a unique island fox evolved from the mainland gray fox [Convergent Evolution] - two different species from different lineages show similar characteristics because they occupy similar environments [Selective Breeding/Artificial Selection] - programs/procedures designed to modify traits in domesticated species - breeders chose desirable phenotypes (leg-length, size, hairiness) A diagram of a plant life cycle AI-generated content may be incorrect. [Homology \| Anatomical] - fundamental similarity due to descent from a common ancestor - ex: same set of bones in the limbs of tetrapod vertebrates has undergone evolutionary change to be used for many different purposes [Homology \| Developmental] - species that differ as adults bear striking similarities during embryonic stages - ex: presence of gill ridges in human embryos indicates that humans evolved from an aquatic animal with gill slits [Homology \| Molecular Homology] - similarities in cells at the molecular level indicate the living species came from a common ancestor or interrelated group of common ancestors - DNA sequences of related species tend to be similar - Ex: p53 proteins play a role in preventing cancer "guarding of genome" → certain genes are found in array of species → sequences of closely related species tend to be more similar to each other than to distantly related species