BIOL 103 Semester Class Notes
BIOL 103 Semester Class Notes 70916 - BIOL 103 - 001
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Lecture- Dr Fondufe Lab- Luis Rodriguez, email@example.com Definition Theme standout Hypothesis vs prediction: - Hypothesis: cheerios make you grow - Prediction: ppl eating cheerios will grow more than ppl eating froot loops 27 August Biology- scientific study of life Common props of all living things: - Order: complex org of living things - Reg of int conds: ability to maintain int enviro consistent w life o Eg workout warm sweat. Thermoregulation - Growth + development: consistent, controlled by DNA - Energy processing: acquiring energy + transforming into useful form [ATP] - Response to enviro: able to resp to enviro stim - Reproduction: produce own kind - Evolutionary adaptation: acquire traits that best suit org to its enviro Emergent properties- w each step in hierarchy of org, new props emerge - Whole > sum of parts Hierarchy of organization: molecule (eg DNA) organelle (eg nucleus) cell (nerve cell) (smallest level w life) tissue (nervous tissue) organ (brain) organ system (nervous system) organism (American alligator) population (all AA living in the wetlands) community (all orgs in wetland ecosystem) ecosystem (Florida everglades. Living and non-living; enviro) biosphere (any place life is possible. All enviros on earth that support life) Cell- basic unit of life. Structural and functional unit of life - Energy processing: cellular respiration- glucose ATP 2 types of cells: - Eukaryotic- eu-karyon = true-nucleus o Membrane-enclosed organelles, incl nucleus w DNA o Eg plants, animals, fungi - Prokaryotic- pro-karyon = before-nucleus o Simpler, smaller o Lack nucleus + other cps (have nucleoid area) o Eg bacteria All cells: - enclosed by embrane (cell membrane, plasma membrane) that regulates passage of materials btwn cell + surroundings - have DNA: genetic info - cytoplasm: btwn nucleus + cell membrane systems biology- models complex interactions of biological systems - functioning of biosphere - molecular machinery of cell correlation of structure + function - related at all levels of bio org - how it’s structured helps its function, eg hands/thumbs 29 August INTERACTIONS: LIVING AND NON-LIVING COMPONENTS Orgs interact w others + w enviro: exch matter/energy - producer: photosysnthesis, prov food in ecosystem - consumer: eat plants/animals - decomposer: decomp waste + remains of dead orgs (nutrients producers) non-living component- chemical nutrients required for life. In soil, air ecosystem must: - recycle the non-living component - move energy through ecosystem chemicals cycle- air/soil plants Animals decomps air/soil energy does not cycle- one way. Sun prods cons heat - enters ecosystem as light, exits as heat - always lose useful energy as useless energy (typ heat) EVOLUTION: CORE THEME OF BIOLOGY Explains unity and diversity of life Based on DNA and common genetic code All cells have DNA: chem substance of genes. Most orgs make proteins from DNA Genes: - unit of inheritance, transmits info parents offspring - grouped into chromosomes, long DNA molecules. Combo of DNA/proteins. Segmented (code for proteins) - control activities of cell species’ gen instructions coded in segs of 4 building blocks. Double-stranded - G: guanine - C: cytosine - T: thymine - A: adenine - G + C and T + A, held together by hydrogen bonds Genome- library of gen instructions an org inherits. Same for skin, hair, liver cells, etc : differential gene expression - We know entire sequence of nucleotides in human genome 2 dimensions of bio: - Vertical: size scale, molecules to biosphere - Horizontal: diversity of orgs existing ever Diversity: hallmark of life - ~1.8 mil species identified and naes - Estimates: 10-100 mil (definition of species accounts for variance in estimates) Taxonomy- name species, classify into groups Kingdoms: - Monera - Protista - Fungi - Plantae - Animalia New thing: domains are bigger than kingdoms - Bacteria: most diverse, widespread prokaryotes - Archaea: prokaryotic like bac. Live in extreme conditions (diff bc of location) - Eukarya: eukaryotic (not all multi-cellular) o Protists (protozoans, algae) o Fungi o Plantae o Animalia Evolution- process of change, transform life from earliest beginnings to diversity of today - Fossil records: been evolving for billions of years, pattern of ancestry 1859: On the Origin of Species by Means of Natural Selection - Ev to support evolution. Today species def “descent with modification” o Mech: natural selection o 2 observations Individual variation: indivs in pop vary in traits, often passed on Overproduction of offspring: more than the enviro can support competition o 2 inferences Unequal reproductive success: traits suited for enviro = most likely to survive. Survival of the fittest Accumulation of favorable traits Natural selection = editing mech, not creating - From exposure of heritable variations to enviro factors that favor some indivs over others DNA divides when cll does: copying mech. Error = mutation Many small changes in population major alterations in species 3 September Numerous small changes in diff populations from natural selection new species (cannot interbreed) - Diversification of species from ancestral species Phylogenetic tree- evolutionary tree showing origin of species Science- “to know.” Is a way of knowing (ToK???) - Based on inquiry, search for info, expl of nat phenom - Scientists typically: o Observe o Hypothesize o Test hypotheses Data- results from experimental observations - Qualitative - Quantitative Inductive reasoning- gen conclusions from many obs - “all organisms are made of cells” Deductive reasoning- specific concs from gen principle - “if all orgs are comp of cells, and all humans are orgs, then all humans are made of cells” - Syllogism - Used in establishing a test of a hypothesis Idea isn’t to prove hypothesis, but to not disprove it Science is repetitive - Hyp supported, exper repeated + verified - Hyp not supported, revises + tested further Theory- - Broader in scope than hypothesis - Gen enough to generate new, specific hyps to test - Supported by large, usually growing body of evidence Science is social: teamwork, share info (peer-review, mtgs, personal comm), build on/conf each other’s work Sci seeks natural causes for natural phenomena - Empirical Controlled experiment- has experimental and control group Evolution: - Core theme of bio - Connected to everyday life - Human selectively breed plants and animals o Humans as agents of evol Antibiotic-resistant bacteria Pesticide-resistant pests Loss of species: habitat loss, global climate change Societal probs- about bio; involve our expanding tech (bio + tech work together) Sci vs tech - Sci goal: understand nat phenom - Tech goal: apply sci knowledge for spec purpose - They’re interdependent o Sci research benefits from new tech o New tech comes from sci research - Eg technology of DNA manipulation results of sci disc of DNA 5 September Darwins origin of species - Defining species - Mechs of speciation Microevolution- change in gene pool of pop from one gen to next Speciation- process by which 1 species 2+ species - Every occurrence = inc in diversity of life - Cause us today, created from ancestors 3.5 billion years ago Species- from Latin “kind” or “appearance” - Defining is difficult because o How similar are members of same species? o Indivs of some species limited in phys appearance variation, others much variation (eg humans) - Appearance + what they’re able to do, incl bird songs, diet, etc Reproductive isolation- prev of mating btwn indivs, prob bc diff species. Pertains to biological species concept - Prev mems of diff species from mating - Prev gene flow btwn species - Maintains sep species - Therefore, diff bc do not share gene pool Biological species concept (BSC)- defines species as: - Group of pops - Mems have potential to interbreed in nature - Prod fertile offspring - Therefore, similar bc reprod w each other - Problematic bc o Can interbreed- hybrids Eg grizzly/polar bears = grolar bears; melting ice = they meet Not a species according to BSC, bc cannot reproduce o Reproductive isolation can’t normally be determined for extinct orgs known only from fossils o Reprod isol =/= prokaryotes or other asexual orgs Morphological species concept- classify by observable physical traits - Applies to asexual orgs + fossils - Subjective Ecological species concept- define by ecological niche - Focus on unique adaptations to particular roles in biological community - 2 are sim in appearance but diff/dist by diet/habitat Phylogeny- looking at evolutionary hist of org or group of orgs Phylogenetic species concept- defines species as smallest group of orgs that shares common ancestor + forms 1 branch of “tree of life” - Trace history by comparing: o Morphology o DNA sequences o Biochemical pathways - Problems: define amt of diff required to dist sep species Sexual + asexual species: morphological, ecological, phylogenetic If identifying new plant species in tropical forest: morphological (not ecological b/c too much time/research) Reproductive barriers- isolate species gene pools. Prevent interbreeding - Prezygotic: before zygote forms (fertilized egg) o Habitat isolation- same general area, not same kind of place o Temporal isolation- breed @ diff times o Behav isolation- little/no “mate recognition” btwn sexes of diff species o Mechanical isolation- organs not compatible o Gametic isolation- gametes (sex cells) not compatible - Postzygotic: after zygote forms o Reduced hybrid viability: don’t develop fully, or don’t survive o Reduced hybrid fertility: vigorous but no viable offspring o Hybrid breakdown: first generation is viable and fertile, but offspring are feeble or sterile Symbiotic relationship- all parties benefit. Eg pollination: hummingbird gets food (nectar), flower reproduces 8 September Sterility of hybrids due to uneven # of chromosomes: can’t make a pair 2 closely related fish live in same lake: 1 along shoreline, 1 bottom feeder in deep water. - Habitat isolation - Prezygotic reproductive barrier MECHANISMS OF SPECIATION BSC key bc focuses on evolution + reproduction Allopatric speciation- populations geographically separated, isolating their gene pools: gene flow is prevented - Allopatric populations: pops sep by geographic barrier - * isolation - * gene pools different - eg Grand Canyon separates 2 types of squirrel: allopatric bc gene flow is prevented. If something like coyote, maybe not separated gene pool bc can cross the canyon sympatric speciation- new species form in the same geographic area - members remain in contact but gene flow reduced: o habitat differentiation o sexual selection o polyploidy- > 2 sets of chromosomes within species (self-fertilization, plants) btwn 2 species (hybridization) diploid (2n)- chromosomes are paired; 2 sets haploid (n)- 1 set of chromosomes. ½ of diploid number gametes chromosome duplication but cell doesn’t divide could lead to tetraploidy (4n) if self-fertilization, resulting 4n zygotes grow into plants that produce fertile 4n offspring by self-fertilization or by mating with other 4n organisms species 2n 4n cells 2n gametes viable 4n offspring tetraploid can’t produce fertile offspring with diploid plant form of tetraploid plant therefore there’s an instantaneous species event- new species, reproductively isolated from parents, created in one generation most polyploids appear when 2 diff species interbreed – hybrid normally sterile bc chromosomes cant pair can reproduce sexually polyploidal speciation more common in plants than animals sympatric speciation in animals is more likely via habitat differentiation or sexual selection than by polyploidy sympatric = living together (sym pops live together) 10 September Sympatric speciation without geographic isolation: - adaptations for exploiting different food sources o if sources in diff habitats, mating = rare o gene pools isolated as each pop adapts to diff resource - sexual selection o appearance/color: bright o “brightly and rightly” colored o Separated based on color- which the females choose - Both contribute to reproductive barriers between allopatric species Reproductive barriers isolate viable fertile polyploidy plant from parental species: hybrid fertility (polyploidy/diploid can’t mate) About 80% of plant species today = descendants of polyploidy ancestors - Hybridization btwn 2 species Most species evolve from allopatric (geog) speciation - Evolution: isolated island chains. Multiple speciation events most likely when: o Physically diverse habitats o Islands far enough apart to permit populations to evolve o Islands close enough for occasional dispersion Because allows potential for mating hybrids Hybrid zones: regions where diff species meet/mate - Recolonization more species: hybrids (as in line above) - 3 possible outcomes: o Reinforcement of reproductive barriers Females can tell males of diff species apart from each other Hybrids less fit than parent species Natural selection reinforces reproductive barriers dec in # of unfit hybrids Barriers btwn species stronger where species overlap (where sympatric) o Fusion: weakening of reproductive barriers Gene flow increases, gene pools increasingly alike Speciation process reversed fuse to one species Cichlid fish, bc pollution murky water can’t tell red/blue apart, behavioral barriers decrease o Stability: continuing formation of hybrid individuals Many hybrid zones are stable Adaptive radiation- evolution of many diverse species from a common ancestor - Radiate from one species because are adapting Galapagos: 14 closely-related finches: Darwin’s finches - Share finchlike traits - Different: feeding habits, beaks, specialized for diet - Arose from adaptive radiation 2 models for tempo of speciation (most evolve from fossils) - Punctuated equilibria model o Change most when arise from ancestral species o Experience relatively little change after that o So, initial drastic change, then fairly stable - More gradual o Fosil records - Total length of time: 4000-400 mil years. HUGE variation. On average, millions of years CHAPTER NINETEEN: MACROEVOLUTION Macroevolution: major changes recorded in history of life over long time span. Contributors: - Continental drift o Crust mantle outer core (liquid) inner core (solid) o Plate tectonics- theory. Giant irregularly shaped plates, float on mantle. Mantle moves, plates move (continental drift) - Mass extinctions - Adaptive radiation - Changes in developing genes 12 September Continental drift: major role in macroevolution 250 mya, Pangea - Biodiversity reshaped - Species to extinction - Provided opportunities to surviving species Mesozoic era: Pangea broke apart geographic isolation Pangea N(Laurasia), S (Gondwana) 65 mya Biogeography- study of distribution of organisms Fossils - Same organisms - Separated by water: may have lived together Diversity of marsupials Extinction inevitable in changing world - Habitat destruction - Environment unfavorable - Predators - Volcanic eruptions Adaptive radiations - Tetrapods - Diversity places to hide Continental drift, extinctions, adaptive radiations: big picture of how changes came about Evo-devo: - Addresses interface of evolutionary and developmental biology - Example: slight generational changes can produce major morphological differences Genes that progress development control rate, timing, spatial pattern of change Paedomorphosis- retention in adult body structures that were juvenile features in ancestral species - Evolutionary alteration of developmental timing - Axolotl calamander- gills in larvae Phylogeny- evolutionary history of species/grp of species - Fossil records - Morphological homologies - Molecular homologies Homologies- similarities due to shared ancestry Homologous structures look and function differently in different species Convergent evolution 15 September Human forearm + bat wings: homologous Bat wing + bee wing: analogous Systematics- discipline of biology, focuses on - Classifying organisms - Determining evolutionary rltnshps: how they differ via taxonomy Taxonomy- Carolus Linnaeus. System of naming/classifying species Binomial- 2-part scientific name: genus, species - Taxon: Each taxonomic unit (kingdom, phylum, etc) - italicize, or underline - capitalize genus, not species phylogenetic tree- depict hypotheses re: evolutionary history of species - branching diagrams reflect hierarchical classification of groups within more inclusive groups - indicates probability of evolutionary relationship, how closely related cladistics- most widely used method in systematics. Groups organisms into clades - clade: group of species, including ancestral species and all of its descendants. Can have a clade within a clade o monophyletic o can use to construct phylogenetic trees - based on Darwinian concept that they can share characteristics w ancestors and still differ (descent with modification) o shared ancestral characteristics: group organisms into clades o shared derived characteristics: novel characteristics distinguishing clades, form branching points in tree of life - important step: compare in group/out group, help identify derived characteristics (evolutionary innovations) that define sequence of branch points in phylogeny o ingroup: taxa whose phylogeny is investigated o outgroup: diverged prior to development of trait parsimony- simplest explanation - typical cladistics analyses involve more complex data, like DNA systematists use many kinds of evidence to construct evolutionary histories - best tree represents the most likely hypothesis based on available evidence. Hypothesis revised, new trees drawn phylogenetic tree of reptiles: crocodilians closest living relatives on birds - 4-chambered hearts - Sing to defend territory - Parental care of eggs within nests - Traits likely present in common ancestor VERTEBRATE EVOLUTION Hypotheses for evolution of chordate groups: - Anatomical evidence - Molecular evidence - Fossil evidence In fig 19.1 on the slide: yellow bars signify the different clades 17 September Hierarchy of clades to which mammals belong: highest to lowest, broadest to narrowest st Lancelet- thought to be 1 group to branch from chordate lineage Transition from water to land: 1. Development of head: craniates 2. Backbone: vertebrates. More extensive skull, backbone/vertebral column 3. Jaws 4. Lungs/lung derivatives 5. Lobed fins w skstetal support 6. Tetrapods: 1 vertebrates on land. Jawed w 2 pairs of limbs 7. Amniotes: tetrapods w eggs adapted for life on land Hagfishes and lampreys: most primitive craniates - Notochord: flexible, supportive rod that runs most of the length of the body - No jaws - Lampreys have rudimentary vertebral structures (vertebrates), hagfishes don’t (invertebrates) Hagfish: deep sea scavengers, produce slime as defense Lampreys: parasites, use tongue to pierce side of fish - Larval: suspension feeders in freshwater streams (receive food floating in water). Feed, buried in sediment Jawed vertebrates: appeared in fossil record approx. 400 mya. Diversified w paired fins and tail: chase wide variety of prey 3 lineages of jawed vertebrates with gills and paired fins, commonly called fishes: - Chondrichthyans- sharks and rays (cartilage) o Most sharks: fast-swimming predators. Vision and smell. Flexible skeleton made of cartilage Electrosensors on heads (sense muscle contractions of prey) Lateral line system: help locate prey via changes in water pressure, vibrations o most rays adapted for life on bottom. Dorsoventrally flattened bodies, eyes on top of head tails: sharp spines, venom glands at base sting painful, sometimes fatal - Ray-finned fishes- tuna, trout, goldfish (most common, what we eat) o Interior skeleton of bone o Fins supported by thin flexible rays o Flattened scales covered w mucus o Operculum- covers a chamber of gills o Swim bladder- lung derivative, helps keep buoyant o >27k species. Most diverse group of vertebrates - Lobe-finned fishes- coelacanths, lungfish (structures to walk on sea floor) o Rod-shaped bones in muscular pelvic and pectoral fins. o 3 lineages: Coelacanths- deep sea, once thought extinct Lungfished- air into lungs, stagnant water in southern hemisphere Tetrapods- adapted to life on land, gave rise to terrestrial vertebrates 22 September Lobe-finned fishes tetrapods. Ancestors of all subsequent groups: amphibians, reptiles Vertebrates had obstacles on land: - Gas exchange - Water conservation - Structural support - Means of locomotion - Adapting sensory organs that worked well in water but not land - Reproduction Acanthostega: fossil that gave concrete evidence that the first tetrapods were fish with necks and 4 limbs that raised their heads above water to breathe oxygen from air, not fish with lungs that evolved legs as they dragged themselves from pool to pool looking for water Environmental conditions that drove evolution: - Warm stagnant water low in oxygen - Ability to supplement oxygen intake by air breathing (head out of water) maybe an advantage - Adaptations allowed them to leave water for long periods diversify rapidly Amphibians - Salamanders, frogs, caecilians - Damp habitats, moist skin supports lungs for gas exchange - Often, poison glands - First to colonize land - Some are only terrestrial or only aquatic Frogs - Mostly on land, eggs in water - Eggs surrounded by moisture so they don’t dry out - Larva (tadpoe) aquatic w gills Reptiles (including birds) and mammals are amniotes - Major derived characteristic: amniotic egg w 4 extraembryonic membranes o Amnion: fluid-filled sac, surrounds embryo o Yolk sac: rich store of nutrients for embryo o Chorion (also allantois): oxygen from air, dispose of CO 2 o Allantois: dispose of metabolic waste Allantois and chorion together: oxygen intake, store metabolic waste - Reptiles include lizards (most numerous and diverse besides birds), snakes (because their ancestors were burrowers), turtles, corcodilians, birds, extinct dinosaurs o Amniotic egg in waterproof shell, skin with scales and waterproofed w keratin, absorb most oxygen via lungs o Lizards, snakes, crocodilians, turtles ectothermic- absorb external heat vs generating their own (cold-blooded) Dinos died out 65 million years ago Most birds can fly - Body changes o Forelimbs feather-covered winds o Large flight muscles: power o Ostrich/emu can’t - Reduce weight for flight: o No teeth o Tail only few small vertebrae o Feathers have hollow shafts o Bones have honeycomb structure: strong but light Flight fast metabolism Endothermic: heat from metabolism. Warm-blooded Efficient circulation/respiratory systems Acute vision, fine muscle control (vision and motor areas show increased development) Complex behaviors especially during breeding seasons Birds evolved from small 2-legged finos, theropods - Archaeopteryx: oldest, most primitive known bird w feathered wings (150 mya) - Look similar to therapods: 2 ft, teeth, wing claws, long tail w many vertebrae o Now, birds 1 vert, small vert - Feathers and scales in reptiles homologous?? Mammals: endothermic amniotes w hair and mammary glands (derived characteristics) - Efficient respiratory and circulatory systems: high metabolism - Teeth differentiated for many kinds of diets: cut, pierce, crush/grind 3 lineages of mammals: - Monotremes o Egg-laying Platypus Echidnas (spiny anteater) o No placenta bc lay eggs o Oldest lineage - Marsupials o Brief gestation o Tiny embryonic offspring pouch, suckle and grow o Placenta o Opossum, kangaroo, koala o Australia, New Zealand, Central/South America o Evolved from eutherians 140 mya - Eutherians o “true placentals”: complete development in utero o Elephant, rodent, dog, cow, human o Placental tissue = maternal and fetal tissue (carrion) First true mammals 200 mya. Small nocturnal insectivores Adaptive radiation after dino extinction large terrestrial carnivores and herbivores, bats, aquatic whales (bc of available niches) Primate: mammalian order - Earliest: small, arboreal, > 65 mya, when dinos were around Arboreal adaptations: - Limber shoulder/hip joints. Climbing and brachiation (branch to branch) - Highly mobile fingers/toes: grasp/manipulate food - Flexible thumb - Short snout, eyes close together: increase depth perception, even if you lose some sense of smell Phylogenetic tree shows 3 groups of primates: - Lemur-loris-potto group o Loris and potto in tropical Africa, South Asia o Lemurs: Madagascar - Tarsiers o Nocturnal, arboreal o SE Asia o Closer to anthropoid that lemur-loris-potto - Anthropoids o Include monkeys/apes w opposable thumb: tip of all 4 fingers touch thumb o Monkeys Old World No prehensile tail Nostrils open downward Eg lion-tailed macaque New World Prehensile tail (grasping) Nostrils wide open, farther apart (more or less flat) Eg golden lion tamarin o Apes Gibbon, orangutan, gorilla, chimp (and bonobo) No tail Relatively long arms, short legs Relatively large brain w respect to body size More flexible behav (can do more) Gorilla, chimp, and human are social o Gibbons Monogamous Only fully arboreal ape Lighter (weight) brachiation o Orangutan Shy, solitary Rainforest trees forest floor o Gorilla Largest Fully terrestrial o Chimpanzee Make and use tools o Human and chimp Closely related: 99% of genes Diverged from common ancestor 5-7 mya Head vertebrae jaws lungs lobe fins (walk) leg amniotic hair and mammary glands 26 September > 500 mya, plants’ algal ancestors: moist fringes of lakes, coastal salt marshes Charophytes- plants and green algae - Evolved from com ances - Multicellular - Photosynthetic eukaryotes Some species accumed adaps live permanently above the water line on land because: - Unlimited sunlight - Plenty of CO 2 - Few pathogens and herbivores (at first) Disadvantages - Maintain cell moisture (don’t dry out). Waxy cuticle cells regulate opening/closing of stomata- guard cells - Support body in nonbuoyant environment - Reproduce and disperse offspring w/out water - Anchor body in soil - Resources from soil (water and minerals) and air (CO , sunlig2t through leaves) Unlike land plants, algae - No rigid tissues - Supported by surrounding water - CO a2d minerals directly from water over whole body - Light and photosynthesis over most of body - Flagellated sperm swim to fertilize egg - Disperse offspring by water Growth-production regions of cell division (apical meristems) near tips of stems and roots Vascular tissue- moves water and minerals from roots to stem/leaf - Xylem- dead cells. Move water and minerals - Phloem- living cells. Move sugars (products of photosynthesis) Veination- pattern of veins Lignin- chemical. Thickens and reinforces cell walls of plant tissues (incl xylem). Polymer. - No lignin in mosses, etc limited height (lack vascular tissue) Distance is important in diffusion All plants: - Gamete and embryo moist - Fertilized egg (zygote) embryo while attached and nourished by parent plant - Alternation of generations: life cycle alts haploid generation (gametophyte generation) which produces egg and sperm and diploid generation, and said diploid generation (sporophyte generation) reproduces via spores within protected structures called sporangia Pollen grains- sperm-producing cells in pines and flowering plants 4 key adaptations distinguish the main lineages: - Dependent embryos present - Lignified vascular tissues mark lineage most living plants - Seeds’ lineage includes gymnosperms and angiosperms - Early diversification seedless, nonvascular bryophytes (no true root/stem, or lignified walls) - Mosses - Liverworts - Hornworts - Have apical meristems and dependent embryos 425 mya vascular w lignin - Seedless vascular included: o Lycophyte (club mosses) o Monilophyte (fern and relatives) - Like bryophytes, moist conditions required for fertilization, disperse offspring in air Vascular w seed evolved 360 mya - Seed- embryo packaged w food supply w/in protective covering - Includes - gymnosperm (ginkgo, cyad, conifer) o older o naked seeds not produced in specialized chambers - angiosperm (flowering trees, grasses) o most abundant o at least 140 mya o flowering plants o seeds in chambers (fruit) ; helps w dispersal Chp 2: Molecules of Cells Big ideas: - elements, atoms, and compounds - chemical bonds (make molecules out of atoms) - water’s life-supporting properties matter- comprises living and non-living things. Anything that occupies space and has mass. Includes air. Consists of elements elements- substance that can’t be broken down to other substances by chemical means. Pure substance, 1 kind of atom - 92 natural - 20 man-made - Abbreviated name is from the English, Latin, or German name Compound- substance of 2 or more elements combined in a fixed ration - Table salt NaCl = 1 sodium 1 chlorine o Na- explosive etal o Cl- poisonous gas o NaCl- edible compound - Characteristics beyond combined elements (greater than sum of parts. Emergent properties) About 25 of 92 natural elements are essential to life 96% of our body weight = C, H, O, N - Other 4% incl phosphorous, sulfur, Ca, K, inter alia 29 September Trace elements- essential to life, but very small amounts - Iron: transport oxygen. Hemoglobin is the molecule that transports oxygen - Iodine: production of thyroid hormones. Deficiency goiter (inflamed thyroid gland) Fluoride to municipal water and dental products to help reduce tooth decay Chemicals to food for nutrition, aesthetics, preservation Atom- smallest particle of matter that still retains the properties of an element - Atom carbon has properties of element carbon - Subatomic particles o Neutron- no electrical charge o Proton- positive electrical charge (+1). One atomic mass o Electron- negative electrical charge (-1). Number of protons, neutrons, electrons differs by element - Helium 2, 2, 2 - Carbon 6, 6, 6 Nucleus of atom: proton and neutron. Teensy tiny. Proton/neutron in central nucleus Electrons in cloud/shell around nucleus - Attracted to nucleus by positively charged protons Nucleus: - Nearly all the weight of the atom (electron weight is negligible) - Proton and neutron approx. same mass - Each proton is one atomic mass unit (amu, 1 dalton) - Each neutron one atomic mass unit (amu, 1 dalton) Atomic number- number of protons in an atom. Unique for each element - Subscript to left of chemical symbol: He,2O, 8 16 - Number of protons/electrons generally the same in an atom o Therefore, atom has no net charge Mass number- number of protons plus number of neutrons - Superscript to left of chemical symbol: He,4 16O, 3S Atomic mass is approximately the same as the mass number # of protons = atomic number # of protons + # of neutrons = mass number Mass number – atomic number = # of neutrons Be able to find the number of neutrons given atomic number/mass number, or #protons and electrons Isotope-variant form of an element: different mass numbers because different numbers of neutrons Isotopes of Carbon: Carbon-12 Carbon-13 Carbon-14 Protons 6 6 6 Neutrons 6 7 8 Electrons 6 6 6 Mass number 12 13 14 Protons = electrons, so neutron must change; only particle that can Isotopes: - Same atomic number (protons), different atomic weights - Same number of electrons, so can react w other atoms in the same way - Some radioactive o Unstable, break down/decay Uses of radioactive isotopes: - Radioactive tracers follow molecules as chemicals change in an organism - Organisms take up radioactive isotopes the same way they take up non- radioactive isotopes - Radiation can be detected by instruments - Medical diagnosis o PET scan detects location of injected radioactive molecules o Heart disorders, cancer, brain Dangers of using radioactive isotopes: - Uncontrolled exposure can damage some molecules in a living cell, especially DNA - Chemical bonds broken by emitted energy formation of abnormal bonds o Replication of damaged cell (still replicates, but replicates the damage now) many damaged cells Photosynthesis: CO +2H O 2 C H 6 12O6 2 CHEMICAL BONDS Atomic structure: electrons - Only particle that comes close enough to others for interaction (think neurotransmitters synapse) o Only particle directly involved in chemical activity of the atom - Arranged in shell, may contain different numbers of electrons - Arrangement determines chemical properties of atom - Periodic table: information about electrons - Fill first shell first, and do least work/use least energy to stay connected. Lowest energy level. Valence shell- outermost shell. Number of electrons determines chemical properties of atom Innermost shell after 2 electrons Shells 2 + 3 (we wont discuss more than 3) can have up to 8 electrons Valence shell full chemically inert/unstable - He, Ne, argon - Doesn’t need to exchange or anything bc already full - Not full, interact: gain, lose, share electrons o Chemical bonds Generally, octet rule: valence contains 8 electrons. Not He or H (2) Covalent bonds- atoms share 1+ pairs of valence electrons - Strongest - 2+ atoms in covalent bond = molecule Compound- 2+ atoms of different elements held together in a fixed ratio Molecule- 2+ atoms of same OR different elements held together by a covalent bond 1 October Covalent bonds can bond atoms of the same element (molecule) or different elements (compound) - Water is a compound (H O) 2 Molecular formula- number/type of atoms in a molecule - H 2 molecular hydrogen Structural formula - H – H o Solid line signifies a covalent bond Single covalent bond = single bond - Shares one pair of electrons (2 total) Double covalent bond = double bond - Shares two pairs of electrons (4 total) Maximum of 2 electrons on innermost shell, generally maximum of 8 on others (octet rule) Some atoms have greater attraction for an electron - Electronegativity- measure of degree of attraction o More electronegative atoms pull harder Nonpolar covalent bond- equal sharing of electrons (not polar; not unequal) - Atoms of same element - Pull towards each atom equally because each atom has same electronegativity o H 2 O 2 - Also some compounds like CH 4 o Difference in electronegativity between C and H is not substantial Polar covalent bond-unequal sharing of electrons (more on one side bc polar) - Atoms w different electronegativity o Water O: high electronegativity (bigger) H: low electronegativity (smaller) o Partial negative charge (bc of presence of electrons) near the strongly electronegative atom o Partial positive charge near weakly electronegative atoms Ion- atom or molecule that has gained or lost an electron and now has an electric charge (whether positive or negative) - Lost electron positive charge - Gained electron negative charge Ionic bond- ions with opposite charge attract NaCl - Na: 1 valence electron - Cl: 7 valence electrons - One electron transfers from Na to Cl o Takes less energy for Na to lose 1 electron than for Cl to gain 7 - Na is now a positively charged ion; has one less negative electron (so balance is in favor of one “extra” positive proton) - Cl is now a negatively charged ion; has one “extra” negative electron Ionic bonds are weak in aqueous environments because ions move apart In living organisms, most of the strong chemical bonds are covalent: link atoms to form molecules Hydrogen atom covalently bonded to one strongly electronegative atom attracted to another electronegative atom: partially charged hydrogen bond - H bonds hold water molecules together (on exam) Remember: 4 molecules bonded to each water Recall: structure of atoms and molecules determines how they behave - Atoms combine to form molecules - H and O can react to form water o 2H 2O 22H O 2 - Balance equation: number and kind of atoms Chemical Reactions Make and Break Chemical Bonds Chemical bonds broken/reformed new arrangements In a chemical reaction: - Reactants- molecules at beginning of equation interact - Atoms rearrange - Products- molecules at end of chemical reaction Rearrange matter: don’t create/destroy Formation of H O from H + O is an example of a chemical reaction 2 C 6 12+ 6_O __2O + __H 2 2 6, 6, and 6 Second blank because there’s C on th6 left Third blank because there’s H 12on the left First blank because there’s more O on the right now after steps one and two Hydrogen bonds and polarity give water its properties, esp hydrogen bonds: key idea Cohesion- tendency for like molecules to stick together - High in H O2 - Most H O2molecules bonded to neighboring molecule at any instant. Bonds are weak and constantly change; bond to different molecules - Due to hydrogen bonds, H O mol2cules are able to travel from plants’ roots up to their leaves Adhesion- tendency for two kinds of molecules to stick together So in a plant, water molecules stick to the cell wall by adhesion, and to each other by cohesion (diagram drawn in notes) 3 October Surface tension- measure of how difficult it is to stretch/break the surface of a liquid - Hydrogen bonding: surface tension is higher in H O tha2 in other liquids - At interface of water and air, H O2molecules are hydrogen bonded to each other and to the water below - Water striders: stand on water without breaking surface o Tips of feet are hydrophobic Thermal energy- energy associated with random movement of atoms and molecules - Called heat when referring to transfer of this energy from warmer to cooler body of matter - Temperature measures the intensity of heat: average speed of molecules in a body of matter o Hotter = faster H 2 can absorb a lot of heat with only a small change in temperature - Allows H 2 to minimize temperature fluctuations - Heat absorbed when hydrogen bonds break - Heat released when hydrogen bonds made - Large body of water absorbs a large amount of heat from the sun in daytime and in summer, but warms only a few degrees - Night and winter, gradually cooling water releases heat to warm the air Earth’s giant water supply moderates temperatures to keep life-sustaining temperatures - Resistance to temp change stabilizes ocean temps good environment for marine life Liquids absorb heat as they evaporate Because of hydrogen bonds, water must absorb an unusually large amount of heat in order to vaporize Water molecule takes energy w it when it evaporates evaporative cooling - Hottest molecules evaporate, cooler molecules stay behind Water: gas, liquid, solid - Less dense as a solid bc of hydrogen bonds o When it freezes, each molecule forms a stable hydrogen bond w 4 neighbors crystal Molecules more spread out in crystal than liquid More molecules in liquid than in solid, because more densely packed o Ice floats bc less dense Protects lakes/oceans from freezing solid Protects aquatic organisms in winter Solution- homogenous mixture of two or more subtances Solvent- dissolving agent (eg water) SOLVent disSOLVes Solute- substance that is dissolved (eg salt, sugar) Aqueous solution- solution w water as solvent How solute dissolves in water: - NaCl ionic bonds, H O 2olar molecule - Pos H ends of H O 2ttract to negative Cl ion - Neg O ends of H O a2tract to positive Na ion - + - So you end up w Cl and Na each surrounded by water molecules: ring of hydration Two categories of substances: - Hydrophilic (water-loving) o Compound w affinity for water o Polar or ionic compounds o Can hydrogen bond with water - Hydrophobic (water-fearing) o Lack affinity for water o Non polar, non-ionic o No hydrogen bonds formed w water Dissociation of H O2 + - - In aqueous solution: small amount dissociates into H and hydroxide, OH - Compound that releases H in a solution is an acid - Compound that accepts H in a solution is a base (has more OH so is able to + accept H ) - Ex acid: hydrochloric acid in water HCl H + Cl+ - - Ex base: sodium hydroxide pH scale- how acidic/basic a solution is - 0 (most acidic) to 14 (most basic) - 7 is neutral. Pure water o [H ] = [OH ]- o Brackets mean “concentration of” pH of most cells kept close to 7 by buffers- substances that resist pH change - Eg blood: maintained at 7.4 CO 2issolves in blood carbonic acid. Buffers come in Buffers accept H when it’s in excess, and donate H when it’s depleted Effects of CO In2rease on Coral Reef Ecosystems CO i2 - Main profuct of fossil fuel combustion - Increasing in the atmosphere - Linked to global climate change About 25% of the CO produ2ed by humans in absorbed by the ocean - Dissolves in seawater pH decreases: ocean acidification - Extra H ions combine with carbonate ions (CO ) to form b3carbonate ions (HCO ) - 2 - Reduces carbonate ion concentration for coral and other shell-building organisms 6 October Isotope- atom of the same element, same atomic number but different atomic mass (eg Carbon-13 has 1 more neutron than Carbon-12) Elements have a unique number of protons (atomic number) Nonpolar covalent bond- 2 atoms share electrons equally Most of the unique properties of water are because molecules are polar and form hydrogen bonds pH1 is 100x more acidic than pH3 (concept on exam) Chp. 3: The Molecules of Cells. Big Ideas: - Introduction to organic compounds - Carbohydrates - Lipids - Proteins - Nucleic acids - (last 4 are 4 classes of biological molecules) Molecular diversity in life is based on the properties of carbon - Carbon-based molecules: organic compounds - Advantage: C can for up to 4 covalent bonds o Therefore build large and diverse organic compounds o Can form 4 CBS because C has 6 electrons. 2 on inner shell, 4 in valence (tetravalent). Each of the 4 on valence can bond o Nice diagram in notes Macromolecule- carbohydrate, lipid, protein nucleic acid Polymer- many units. Some macromolecules are made from identical or very similar building blocks strung together Monomer- building blocks for polymers - Dehydration reaction/synthesis (mean the same thing)- monomers linked together, water removed. Each linking removes 1 H O. pol2merization - Nice picture in notes Hydrolysis (breaking polymers)- water is added Starch is too big to enter cell: hydrolysis changes it into glucose - Store unused glucose as glycogen in skeletal muscles (movement) Dehydration reaction and hydrolysis both require enzymes - Molecules that speed up chemical reactions in cells Cells make large number of polymers from small group of monomers - Proteins made from only 20 different amino acids - DNA made up of 4 kinds of nucleotides Monomers used to make polymers are universal Carbohydrates: can be anything from small sugar molecules to large polysaccharides - Monosaccharide: monomers of carbs. Simple sugars o Glucose, fructose o Hook together more complex sugars and polysaccharides o Major nutrients for cells - Disaccharide: composed of 2 monosaccharides o linked together by covalent dehydration bond (dehydration bond is covalent) o sucrose (table sugar) = glucose + fructose o lactose (milk sugar) = glucose + galactose o maltose (malt sugar) = glucose + glucose - polysaccharide: polymers of many monosaccharides o 100s to 1000s of monomers linked by dehydration reaction o Storage molecule, structural compound Starch is storage form of glucose in plants Glycogen is storage form of glucose in animals. Stored in liver and muscle tissue. Cellulose: structural component of plant cell walls. Polymer of glucose Humans cannot digest (fiber). Lack cellulase enzyme Cows and termites have microorganisms that digest cellulose Decomposing fungi can digest cellulose Chitin: structural. Forms exoskeletons of insects and crustaceans. Used in some biodegradable surgical thread Lipid- diverse compound, mainly C + H atoms linked by nonpolar covalent bonds - Not true polymers (question on exam!) o Can have large chains, not linked by covalent bonds o Grouped together bc hydrophobic o Fats, phospholipids, steroids - Fats: triglycerides bc formed of glycerol linked to 3 fatty acids by dehydration reaction o Hydrolysis fatty acids and glycerol o Oil: liquid fat 8 October Functions of fat: - Energy reserve (major function) o 1g of fat stores twice as much energy as 1g of polysaccharide o Mammals store in adipose tissue: subcutaneous layer - Insulation - Cushions vital organs Saturated fatty acids/fats - Maximum number of H atoms o “saturated” with H - Only single covalent bonds between carbon atoms - Most animal fats - Usually solid at room temperature o Butter o Beef fat - Maybe cardiovascular disease (um no) I have a really nice picture of saturated/unsaturated molecules in my notes. Includes unsaturated is liquid at room temperature bc a double covalent bond creates a bend or kink in the molecule, not allowing them to stack together so nicely Atherosclerosis- artery blocked by plaque - Less room for blood to get through, like thumb over a hose: blood pressure increases Unsaturated fatty acids/fats - Does not have the maximum number of H atoms - At least 1 double covalent bond between carbon atoms - Plant/fish oils - Usually liquid at room temperature Hydrogenated vegetable oils - Unsaturated fat becomes saturated fat by adding H - Hydrogenization creates trans fats - Trans fats heart disease 1890s, process of adding H to unsaturated oils because - Reduce oil spillage - Help withstand heating for frying - Decrease consumption of animal fats (they thought it was unhealthy) 1990s, partially hydrogenated oils were common in cookies, crackers, bread Trans fat worse than saturated fat - 1 study: eliminating trans fats can stop up to 1/5 of heart attacks - 2006 FDA requires listing trans fats on food labels - City/state laws eliminate trans fats in unlabeled foods like in restaurants and schools - Some countries banned trans fats Monounsaturated fats: 1 double bond Polyunsaturated fats: many double bonds Phospholipids - 2 fatty acid tails attached to glycerol (vs triglycerides, these are diglycerides) - Phospholipid bilayer is major component in cell membranes - Hydrophilic head (glycerol) I contact w environment and internal part of cell - Hydrophobic tail in center of layer - Pretty drawing in my notes Cell membrane = plasma membrane =/= cell wall - Everything has a cell membrane/plasma membrane - Only plants have a cell wall: cellulose Steroid- lipid with carbon skeleton and 4 fused rings - Ex cholesterol o Significant role in structure of animal cell membranes o Starting material for making other steroids, including sex hormones o High levels in blood can lead to circulatory disorders - Estradiol (estrogen) o Female sex hormone - Testosterone o Male sex hormone - Nice drawings of estrogen and testosterone in notes! Recall: carbohydrates’ monomers = monosaccharides Anabolic steroids- synthetic variants of testosterone - Testosterone causes buildup of muscle/bone mass in males in puberty, and causes them to maintain masculine traits throughout life - Sold as prescription drug, treats certain diseases - When abused, can cause mood swings, depression, liver damage/cancer, testicle shrinkage, reduced sex drive Proteins- derived from Latin for first place - Very important macromolecules - Carry out most of the functions of cells - Tens of thousands of different proteins - Each kind has a specific 3-D shape that corresponds to its particular function - Polymer made from amino acid monomers Examples: - Enzyme: speed rate of chemical reaction o Most important role of proteins - Structural (hair, connective tissue) - Contracticle (muscle cells) - Defensive (antibodies) - Signal (hormones) - Receptor proteins in cell membranes - Transport (hemoglobin) - Storage (ovalbumin- egg) Protein lysozyme: takes up bacteria (antibacterial) - Ribbon model and space-filling model both show grooves where they take up bacteria Spiderweb: fibrous silk proteins - Stronger for its weight than steel 10 October Denaturation- unfolding of a protein - Protein unravels, loses shape and therefore its function - Caused by pH change, temperature (that’s how fevers kill you!) Proteins are most diverse molecules re: structure and function Peptide bonds- covalent bonds that link amino acids Protein diversity is based on different arrangements of only 20 amino acid monomers Cells link amino acids together by dehydration synthesis, creating polypeptides Polypeptide- linking of amino acids - Chain consists of 100s/1000s of amino acids linked by peptide bonds - Each has unique sequence of amino acids - Think of amino acid as a thread, polypeptide as yarn, and protein as sweater Functioning protein consists of at least one polypeptide chain coiled, twisted, folded into unique shape particular 3D shape determines function Four levels of protein structure Primary structure- combination of amino acids - Unique amino acid sequence - Linear arrangement of amino acids held together by peptide bonds - Correct sequence is determined by DNA - Slight changes in sequence can affect protein’s ability to function o Sickle-cell hemoglobin Secondary structure- individual folds - Results from coiling/folding of the polypeptide chain o Coiling helical structure alpha helix o Folding beta pleated sheet 1 polypeptide folds on self, neighboring pieces hydrogen bond - Alpha helix and beta pleated sheet both stabilized by hydrogen bonds Tertiary structure- overall shape - Overall 3D shape of polypeptide (determines function of protein) - Held together by various bonds/interactions o Hydrogen o Ionic o Covalent Quaternary structure- combination of polypeptides - Applies only to proteins consisting of more than one polypeptide chain o Chains aggregate into one functional macromolecule o Examples: Collagen: 3 polypeptide chains Hemoglobin Transthyretin: transfer protein Nucleic Acids DNA- deoxyribonucleic acid RNA- ribonucleic acid Stretches of DNA = genes. Program amino acid sequences of proteins - Gene- unit of inheritance DNA- genetic material inherited from parents - Includes directions for own replication - Programs cell’s activities by directing protein synthesis Genetic info flows DNA RNA protein Genes- segments on DNA able to code for particular proteins Have exact same genes I every cell in body: differential gene expression Flow of genetic info from DNA RNA = transcription Flow of genetic info from RNA protein = translation Ok so think DNA and RNA are both nucleic acids, so it’s transcribed from one medium to another, but it has to be translated to protein because it’s such a different form; not a nucleic acid Informational polymer - Monomer = nucleotide Polymer (aka polynucleotide) formed by dehydration synthesis Sequence of nucleotides stores genetic info Nucleotide composed of three parts - 5-carbon sugar called ribose in RNA and deoxyribose in DNA - Phosphate group - Nitrogenous base o DNA: Adenine Thymine Cytosine Guanine o RNA: Adenine Uracil Cytosine Guanine o Difference DNA/RNA is T in DNA, U in RNA Polynucleotide forms from the nucleotide monomers when the phosphate of one nucleotide bonds to the sugar of the next nucleotide - Results in a repeating sugar-phosphate backbone with protruding nitrogenous bases o Its like one side of the double helix. Looks like: |- DNA is two polynucleotide strands twisted around each other in a double helix - Hydrogen bonds between A and T, C and G RNA is usually single-stranded polynucleotide Majority of ppl stop producing enzyme lactase in early childhood, don’t easily digest milk sugar lactose - Intolerance is normal Tolerance is a relatively recent mutation in genome. Survival advantage for cultures w dairy available year-round Lactose intolerance involves which 3 of the 4 major classes of biological molecules? - Protein: enzyme to digest the lactose - Carbohydrate: lactose is sugar - Nucleic acid: DNA changes/mutates to allow for tolerance 14 October Base-pairing rule- - A pairs with T - G pairs with C They’re complementary Sugar-phosphate backbone held together by covalent bonds Nucleic acids held together by hydrogen bonds Big Ideas - Introduction to the cell - Nucleus and ribosomes - Endomembrane system - Energy-converting organelles - Cytoskeleton and cell surfaces Microscopes- clearer views of cells and cellular structure 2 important factors of microscopy - Magnification: increase in size of object - Resolution: measure of image clarity: ability of instrument to show two close objects as separate Light microscope (LM)- most used - Light: specimen glass lens eye - Magnifies up to 1000x, resolution about 0.2µm (micrometer) o Thus cannot provide details about a small cell’s structure: limitation of LM - Led to cell theory: o Cells are fundamental units of life o All living things are composed of cells o All cells come from other cells Electron microscope (EM)- very powerful: ultrastructure of cells - Uses beam of electrons, not light - Can resolve (resolution) biological structures as small as 2 nanometers (100- fold improvement over light microscope) - 2 types: o Scanning electron microscope: cell surfaces o Transmission EM: internal cell structure - Limitation: cannot be used to study living organisms Can’t see most cells with naked eye - Most are 1-100µm in diameter - Bacteria are smallest - Plant/animal cells 10 times larger than bacteria 1000 nm per µm 1000 µm per mm Cells must be big enough to house DNA, proteins, and structures needed to survive and reproduce, but small enough for a surface-to-volume ratio with adequate exchange with environment - Surface area is important for functioning, including acquisition of nutrients/oxygen, removing waste o Increase in size means the volume increases faster than the SA o SA/V ratio decreases as size increases Small cell has more SA relative to V: more efficient Plasma membrane- boundary between cell and its surroundings. Controls movement of molecules in and out of cell - Made of lipids, proteins, some carbohydrates o Most abundant lipids: phospholipids Channel proteins are hydrophobic internally, hydrophilic externally - Allow ions and other hydrophilic molecules to pass through hydrophobic molecules to pass through hydrophobic center of membrane Peripheral proteins attached to membrane surface. Serve as pumps: use ATP to actively transport molecules into/out of cell All cells (prokaryotic or eukaryotic): - Plasma membrane - Cytosol: internal. Thick, jelly-like liquid - Chromosomes: 1+ made up of DNA - Ribosomes: tiny structures that make proteins Eukaryotic cells: - Membrane bound nucleus o Holds most of the DNA - Membrane enclosed organelles o Perform specific functions in the cell - Cytoplasm: region between nucleus and plasma membrane o Houses various organelles Prokaryotic cells: - Nucleoid region: houses DNA. No membrane - Cytoplasm: interior of cell. - Most have cell wall: protect, help maintain shape of cell - Capsule: some. Sticky coat, helps protect cell and glue cell to surfaces - Surface projections: some o Short fimbriae: help to attach to each other or to substrate o Longer flagella: help move cell around liquid environment 15 October Penicillin attacks enzyme used to make cell walls Bacterial ribosomes =/= eukaryotic ribosomes Eukaryotic structures and organelles are organized into 4 basic groups: - General control o Nucleus o Ribosomes - Manufacturing, distribution, breakdown of molecules o Endoplasmic reticulum o Golgi apparatus o Lysosome o Vacuole o Peroxisome - Energy processing o Mitochondria o Chloroplasts - Structural support, movement, communication o Cytoskeleton o Plasma membrane o Plant cell wall Membranes separate eukaryotic cells into compartments, where cellular metabolism takes place - Each compartment is fluid-filled, maintains conditions for particular metabolic processes and activities - cellular metabolism: chemical activities of a cell in a plant cell,
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