ENV 226: Essential Ecology Final Exam Study Guide — om single-species thinking to the dynamics of many interacting ecies. A community is more even when all species have similar abundances. Diversity: A combined measure of richness and evenness. More diverse = more likely to pull multiple different species out of a 'hat'. Shannon Diversity Index (H′): The most common diversity index. Higher H′ = more diverse (high richness AND high evenness). Formula: H′ = –Σ(pᵢ · ln pᵢ), where pᵢ is the proportion of individuals in species i. Worked example If a community has 4 species, each at 25% (p = 0.25), then H′ = –[4 × (0.25 × ln 0.25)] = 1.39. If one species dominates (e.g., 70/10/10/10), evenness drops and H′ falls even though richness is the same. Why diversity matters — ecosystem function & services Ecosystem function: Biological, geochemical, and physical processes that take place within an ecosystem (e.g., productivity, nutrient cycling, decomposition, pollination). Ecosystem services: The benefits humans derive from ecosystems. Four major categories: Provisioning: food, water, timber, fiber Regulating: climate regulation, flood control, water purification Cultural: recreation, spiritual, aesthetic, educational values Supporting: soil formation, nutrient cycling, primary production How diversity affects function — mechanism Complementary resource use (niche complementarity): Different species use slightly different resources (e.g., water at different soil depths, nutrients at different times). A diverse community captures more of the available resources than any single species could, raising total productivity. Diversity–stability theory Compensation: Species respond differently to environmental fluctuations. When one species declines, another can increase and 'compensate,' keeping overall ecosystem function steady. Insurance hypothesis: A diverse community is more likely to contain at least one species with traits that help the ecosystem cope with change. Diversity acts as ecological 'insurance' against disturbance. Rules of community assembly — what determines diversity at a site Three filters act in sequence on the regional species pool to determine which species actually end up in a local community: Term Definition Dispersal Who can physically get there. Controlled by distance from source populations and by dispersal ability. Connects to the 'mass effect' / rescue effect — regional diversity (gamma) can rescue local diversity (alpha). Environmental filtering What species can tolerate the abiotic conditions (climate, soil, water, salinity). Example: Ponderosa pine will not survive in the Sonoran Desert — environmental filtering excludes it. Biotic filtering What species can coexist given interactions with other species (competition, predation, facilitation). Strongest where abiotic conditions are benign, because more species can be there to interact. Intertidal zonation paradigm — how the filters stack In rocky intertidal communities, abiotic stress (desiccation, wave action) sets the UPPER limit of a species' distribution — an environmental filter. Competition and predation set the LOWER limit — biotic filters. Take-home: environmental filtering dominates in stressful zones; biotic filtering dominates in benign zones. What maintains diversity Intermediate Disturbance Hypothesis (IDH): Diversity is highest at intermediate frequencies or intensities of disturbance. Low disturbance lets competitive dominants exclude others; high disturbance eliminates all but the most disturbance-tolerant species. The middle keeps both groups in the community. Positive species interactions (facilitation): When one species makes conditions better for another (e.g., a nurse shrub providing shade and moisture for seedlings underneath). Facilitation tends to INCREASE biodiversity, especially in stressful environments. 1.2 Succession Primary succession: Colonization of a substrate that has NEVER supported life (e.g., bare bedrock, new volcanic rock, glacial retreat). Soil must be built from scratch, typically by pioneers like lichens and mosses. Secondary succession: Recovery after a disturbance that left soil and some biological legacy behind (e.g., a cleared field, most wildfires). Much faster than primary succession because soil and seed bank persist. Pioneer species: The first species to colonize a disturbed or bare area. Typically fast-growing, high-dispersal, stress-tolerant organisms that modify the site so later-successional species can establish. Quiz-style example The Woodbury Fire burned so intensely on the Tonto NF that only bedrock remained. Recolonization of this area is PRIMARY succession — there is no soil or seed bank left to start from. 1.3 Ecological Energetics Energy: The currency of ecosystems. Most ecological energy originates from the sun as electromagnetic radiation and is stored in tissues (biomass). Trophic level: Organisms that share the same function in the food chain and the same nutritional relationship to primary sources of energy. Level 1 = producers; 2 = primary consumers (herbivores); 3 = secondary consumers (carnivores); 4+ = tertiary / apex predators. Autotroph (primary producer): An organism that produces its own food from inorganic sources — typically plants, algae, and some bacteria via photosynthesis. Consumer (heterotroph): An organism that obtains energy by consuming other organisms. Primary consumers eat producers; secondary consumers eat primary consumers; etc. Production: The rate at which new biomass is created by organisms in an ecosystem (units of mass or energy per area per time). Net primary production (NPP): Gross primary production (total photosynthesis) MINUS the energy plants use for their own respiration. NPP is what is actually available to herbivores. Assimilation and production efficiency Energy is lost at every step of the grazing food chain. Two key efficiencies describe where energy goes: Term Definition Assimilation efficiency (Energy assimilated / energy consumed) × 100%. Assimilated = consumed – egested (waste). Herbivores ≈ 20–50% (tough plant material); carnivores ≈ 80% (similar tissue chemistry). Production efficiency (Energy in new biomass / energy assimilated) × 100%. Endotherms (birds, mammals) are LOW (~1–3%) because most energy is burned as heat; ectotherms (insects, reptiles, fish) are HIGH (~10–50%). Worked example (assimilation efficiency) Eats 400 J, excretes 200 J as waste, puts 50 J into growth. Assimilated = 400 – 200 = 200 J. Assimilation efficiency = 200 / 400 = 50%. The 10% rule Roughly 10% of the energy at one trophic level is transferred to the next. The rest is lost to respiration, heat, and waste. This is WHY food chains are short (usually 4–5 links): there simply isn't enough energy left to support another level. 1.4 Food Webs A food web is many, connected food chains — a map of who eats whom across an entire community. In simple diagrams, arrows point from prey to consumer. Complex diagrams use plus/minus signs to show the direction of effect, and dashed lines to show indirect effects. Top-down control: Higher trophic levels (predators) limit the abundance of lower levels. Removing a top predator releases herbivores, which suppress plants. Bottom-up control: Lower trophic levels (nutrients, producers) limit higher levels. Adding nutrients increases plants, which increases herbivores, which increases predators. Trophic cascade: Indirect effects of a predator propagate down the food web. Classic example: wolves reintroduced to Yellowstone → elk browsing decreases → riparian willow and aspen recover → beavers return → stream ecosystems recover. 2. Ecosystems Ecosystem: A community of organisms PLUS their shared environment. Includes biotic components (plants, herbivores, carnivores, detritivores) and abiotic components (climate, soils, nutrients). 2.1 Ecological building blocks Ecological building block: An atom that (1) makes up organisms and (2) is relatively abundant. Key building blocks: C, H, O, N, P (and sometimes S) — collectively CHONP. Not building blocks: Silicon, aluminum, arsenic, tungsten — they may be abundant in the crust or used by some organisms, but are not core structural elements of life. Potassium is important biologically but is NOT a core 'ecological building block' in this course's sense. 2.2 Liebig's Law of the Minimum Growth is dictated not by the total resources available, but by the SCARCEST resource. The 'limiting nutrient' sets the ceiling on production; adding more of a non-limiting nutrient has no effect until the limit is raised. Application — nutrient pollution A coastal system receives 10 g N, 200 g P, 50 g C, and 20 g O per year as pollutants, and you know the system is N-limited. By Liebig's Law, adding MORE nitrogen is what will most change structure and function — even though phosphorus is arriving in larger quantities, it is not the limiting nutrient. 2.3 Eutrophication Eutrophication is the enrichment of an aquatic system with nutrients (especially N and P) from fertilizer runoff, wastewater, or atmospheric deposition. Process: Excess N fuels algal blooms → algae die and sink → microbial decomposition consumes oxygen → a hypoxic 'dead zone' forms → fish and invertebrates die. Once N is drawn down, the system can become P-limited; phosphorus mined for fertilizer keeps the cycle going. The Gulf of Mexico hypoxic zone is the classic example. 2.4 Nutrient cycles (N, C, P) Term Definition Nitrogen cycle N₂ in atmosphere is biologically inert. Nitrogen-fixing bacteria (free-living and in legume root nodules) convert N₂ → ammonium (NH₄⁺). Nitrification converts NH₄⁺ → nitrite → nitrate (NO₃⁻), the form most plants take up. Denitrification returns N₂ to the atmosphere. Humans roughly DOUBLED global N fixation via the Haber-Bosch process → fertilizer → eutrophication. Phosphorus cycle Largely a SEDIMENTARY cycle — no gaseous phase. P weathers from rock → soil → plants → consumers → back to soil → eventually to ocean sediments. Slow turnover at global scales; a critical component of DNA/RNA, phospholipids, bones, and ATP. Carbon cycle See dedicated section below. C moves among atmospheric, terrestrial, oceanic, and fossil pools. Photosynthesis pulls CO₂ out; respiration and combustion return it. 2.5 Ecotones and cross-ecosystem flows Ecotone: A transition zone between two ecosystems, exhibiting gradients in environmental conditions and a related shift in the composition of plant and/or animal communities (e.g., forest–grassland edge, estuary). Two factors determine how a flow of material/energy from one ecosystem affects another: Relative size of the systems — when the amount of something varies across ecosystems, the LARGER system has a bigger impact on the small system (e.g., a stream flowing into a small pond vs. into the ocean). Quality of the resource — rich subsidies (like salmon carcasses bringing ocean nutrients to streams) matter more than dilute ones. 2.6 Ecological state change & resilience Key components of ecosystems: STRUCTURE (what organisms are there and how they interact), FUNCTION (processes of energy and nutrient movement), and REGIME (which of several possible stable states the system is in). Alternative stable states: An ecosystem can exist in two or more contrasting conditions under the same environmental conditions (e.g., clear lake vs. turbid lake; forest vs. shrubland). Ecological state change (regime shift): A large, persistent, often abrupt shift in the structure and function of an ecosystem, triggered by crossing a critical threshold. Threshold / tipping point: The level of a driver (stressor) at which a system flips to a new state. Hysteresis: Once a system flips, simply reversing the driver does NOT restore the original state — the return path is different from the 'forward' path. Slow vs. fast drivers: Slow drivers (e.g., gradual warming, soil nutrient accumulation) build up until a fast driver (e.g., fire, storm) tips the system across the threshold. Perturbation: Any event (abiotic or biotic) that disturbs the ecosystem. Perturbations that cause regime change can be abiotic (fire, flood, drought) or biotic (pest outbreak, invasion). Resilience: The capacity of a system to absorb disturbance, adapt to change, and recover from adversity while maintaining its essential functions, structure, and identity. The ball-and-cup diagram Picture a ball sitting in a valley (cup) on a hilly landscape. The ball is the current state of the ecosystem; the cup is the 'basin of attraction' for that state. A disturbance pushes the ball; stabilizing (negative) feedback loops pull it back. Strong disturbance or a shrinking cup (loss of resilience) can push the ball over a hill into a NEW cup — that's state change. Negative (stabilizing) feedback loop: A change triggers a response that DAMPENS the change, keeping the system near its current state. Deepens the cup. Positive (amplifying) feedback loop: A change triggers a response that AMPLIFIES the change, pushing the system further from its current state. Flattens the cup and makes state change more likely. Applying resilience to conservation & restoration Manage for resistance — remove stressors that push the ball (exclude high-intensity grazing, reduce pollution). Manage for resilience — rebuild the 'cup' by re-establishing key species, nutrient cycling, and stabilizing feedbacks (planting perennial grasses, restoring hydrology). Passive restoration works when the seed bank, soil, and key species are still intact; active restoration is needed when the system has already crossed the threshold. 3. Landscape Ecology and Biogeography 3.1 Landscape ecology Landscape ecology: The study of spatial patterns of ecosystems and their ecological consequences — explicitly considers the arrangement of habitats across space and how organisms and materials move through them. Spatial elements Term Definition Patch A relatively homogeneous area that differs from its surroundings (e.g., a forest stand in a grassland). Generally the highest-quality habitat. Matrix The background land-cover type that surrounds patches (e.g., desert in Saguaro NP, or agricultural land around forest fragments). Corridor A linear feature connecting patches — allows movement of organisms, genes, and energy. Examples: riparian strips, hedgerows, engineered wildlife crossings (Oracle Road, Tucson). Ecotone See above — the transition zone between landscape elements. Spatial heterogeneity Variability in environmental conditions and habitat types across a landscape. Drives diversity at landscape scales. Scale dependence Ecological patterns and processes depend on the spatial/temporal scale at which they are observed (e.g., a species may look stable regionally but be declining locally). Fragmentation Fragmentation breaks a large continuous habitat into smaller, more isolated patches. Effects include: Loss of total habitat area More edge relative to interior — edge effects (different microclimate, invasives, more predators) penetrate into remaining patches Reduced connectivity — animals cannot move between patches Smaller populations in each patch → inbreeding depression, loss of genetic variability, higher extinction risk Saguaro NP example Mid-sized carnivores in Saguaro NP West crashed after a disease outbreak and never recovered. Why? The city of Tucson grew between Saguaro NP East and West, severing connectivity. No recolonization could occur from the eastern population. Solution: re-establish connectivity — the Oracle Road wildlife crossings documented over 4,400 crossings by 16 species in their first two years. Patch dynamics Patch size, shape, and connectivity change over time because of ecological processes — succession, disturbance (fire, flood, windthrow), and fragmentation — not random chance and not just geology. 3.2 Biomes and realms Biome: A large biological community defined by climate and dominant vegetation type (e.g., tropical rainforest, boreal forest, tundra, desert, savanna, temperate grassland). Biogeographic realm: A large area of the Earth's surface with a distinctive assemblage of taxa, reflecting shared evolutionary history (e.g., Nearctic, Neotropical, Palearctic, Afrotropical, Indomalayan, Australasian, Oceanic, Antarctic). Factors shaping where biomes are found: temperature and precipitation (the primary controls), seasonality, latitude, elevation, continental geography, and evolutionary history. Realms reflect plate tectonics — Pangaea split into Laurasia and Gondwana, then into the continents we have today, producing unique evolutionary trajectories in each realm (e.g., Australia's marsupials, Madagascar's lemurs). 3.3 Island Biogeography and the SLOSS debate MacArthur & Wilson's Theory of Island Biogeography: species richness on an island is set by the balance between the colonization rate (immigration) and the extinction rate. Size effect — larger islands have LOWER extinction rates (bigger populations). Distance effect — islands closer to the mainland have HIGHER colonization rates. Equilibrium species number occurs where colonization and extinction curves INTERSECT. SLOSS debate — Single Large Or Several Small? Originally framed: is a single large reserve or several small reserves of equal total area better for biodiversity? Large favors: lower extinction, room for interior species, bigger populations, full food webs. Several small favors: replication (insurance against one disaster), sampling more habitat types, potentially higher total diversity. Modern answer: it depends — on species' dispersal, the matrix, and whether you value diversity vs. viability. Connectivity (corridors) often matters more than the large/small question alone. Source population: Produces more offspring than can be supported locally — exports individuals to other patches. Population growth rate > 0. Sink population: Organisms arrive but do not reproduce enough to sustain the local population; persists only via immigration from sources. Population growth rate < 0. 4. Extinction and Climate 4.1 The 'Big Five' mass extinctions Term Definition Ordovician–Silurian (~439 Mya) ~85% marine species lost. Cause: rapid glaciation and sea-level drop, then warming. Late Devonian (~364 Mya) Prolonged event; major loss of marine invertebrates, especially reef builders. Probable causes include ocean anoxia and climate change. Permian–Triassic (~251 Mya) 'The Great Dying' — ~96% marine species and ~70% terrestrial vertebrates. THE most severe. Cause: Siberian Traps volcanism → CO₂ spike → warming, ocean acidification, and anoxia. Recovery took 5–10 million years. End Triassic (~199–214 Mya) ~50% of species lost; cleared the way for dinosaurs to dominate. Likely cause: CAMP volcanism and climate change. Cretaceous–Tertiary (K-Pg, ~65 Mya) ~76% of species, including non-avian dinosaurs. Cause: Chicxulub asteroid impact (plus Deccan Traps volcanism) → darkened skies, cooling, then warming. Why scientists are concerned now Current extinction rates are 100–1000× background rates — comparable to mass-extinction levels. Rate of change: current climate change is occurring more rapidly than almost any past episode — faster than many species can adapt or track. Humans have built roads, cities, and agricultural landscapes that BLOCK the range shifts species would otherwise use to follow their climate. Human societies are themselves adapted to current climate (agriculture, supply chains, coastlines) — disruption drives conflict. 4.2 Why climate change affects ecological systems Temperature, precipitation, seasonality, and extreme events all drive the distribution and performance of every species. Shifting climate disrupts energy balance, water balance, food availability, and reproduction; changes the timing of seasonal events; and alters disturbance regimes (fire, floods, storms). All of these cascade through communities and ecosystems. 5. Climate Change — Ecology, Climate, and the Carbon Cycle 5.1 The carbon cycle Term Definition Pool (reservoir) A place where carbon is stored and from which it can be released. Measured as a quantity (e.g., gigatons). Flux The amount of carbon exchanged between pools per unit time (gigatons/year). Measures MOVEMENT. Sink A pool that accumulates more carbon than it releases — net REMOVER of carbon from the active cycle. Source A pool that releases more carbon than it accumulates — net ADDER of carbon to the active cycle. Biggest/smallest pools & fluxes Major carbon pools (approximate, gigatons): Deep ocean: ~37,000 GtC — BY FAR the largest pool Fossil pool (oil, gas, coal): ~10,000 GtC — second largest Reactive ocean sediments: ~6,000 GtC Soils: ~2,300 GtC Surface ocean: ~1,000 GtC Atmosphere: ~800 GtC — this is the pool that drives climate Plant biomass: ~550 GtC (the largest LIVING pool) Major fluxes are photosynthesis and respiration (~120 GtC/yr terrestrial; ~90 GtC/yr ocean), which are normally nearly balanced. Fossil-fuel combustion and deforestation are the (smaller but crucial) fluxes currently unbalancing the system. Why atmospheric CO₂ is increasing Humans are burning fossil fuels — moving carbon from a long-term sink (the fossil pool) into the active atmospheric pool faster than natural sinks can remove it. Deforestation and land-use change also shift carbon from plant biomass and soils to the atmosphere. The balanced photosynthesis/respiration fluxes cannot keep up with the ~10 GtC/yr added by human activity. 5.2 Ocean acidification As atmospheric CO₂ rises, more CO₂ dissolves into the ocean. The chemistry: Step 1: The ocean is slightly alkaline; CO₂ is slightly acidic, so CO₂ dissolves into seawater. Step 2: CO₂ + H₂O → H₂CO₃ (carbonic acid). Step 3: H₂CO₃ dissociates → HCO₃⁻ (bicarbonate) + H⁺. Step 4: Some HCO₃⁻ dissociates → CO₃²⁻ (carbonate) + H⁺. Step 5: Bicarbonate and carbonate exist in equilibrium. Net result: more H⁺ ions → lower pH = acidification. Acidification also reduces carbonate availability, making it harder for corals, shellfish, and plankton to build calcium-carbonate skeletons. Warming and the ocean's ability to sequester carbon Warmer water holds LESS dissolved CO₂ (inverse solubility). As oceans warm, their ability to absorb atmospheric CO₂ decreases — a positive feedback loop that further increases atmospheric CO₂ and warming. 5.3 Important climate feedback loops Term Definition Ice-albedo feedback (POSITIVE) Warming melts polar ice → darker ocean/land replaces reflective white ice → lower albedo, more solar energy absorbed → more warming → more melting. Water vapor feedback (POSITIVE) Warming increases evaporation; water vapor is a greenhouse gas → more warming → more evaporation. Permafrost/methane feedback (POSITIVE) Thawing permafrost releases CO₂ and CH₄ long locked in frozen soils → more warming → more thawing. CO₂ fertilization (NEGATIVE, partially) Higher CO₂ can boost plant photosynthesis, pulling more C out of the atmosphere. Partially counteracts warming but is limited by water, nutrients, and heat stress. Ocean solubility feedback (POSITIVE) Warmer oceans hold less CO₂ → more stays in the atmosphere → more warming. Quiz-style example Melting polar ice caps → decreased albedo → further warming = POSITIVE feedback loop (amplifies the original change). 5.4 Factors affecting Earth's surface temperature Three major controls: Energy arriving from the sun (solar radiation) Earth's albedo — how much of that energy is reflected back to space Greenhouse gases in the atmosphere — how much outgoing infrared is trapped Carbon dioxide is the LARGEST driver of current human-caused climate change (sheer volume, long atmospheric lifetime). Methane is more potent per molecule but far less abundant; water vapor amplifies change via feedback but is not itself a primary driver. 6. Climate Change — Ecological and Human Response 6.1 How climate change affects plants and animals Climate change disrupts performance in three main ways: Term Definition Energy balance Plants: respiration rates rise faster than photosynthesis with warming — net carbon gain (and growth) drops. Animals: thermoregulation costs rise; outside the thermal neutral zone, organisms burn more energy just to stay alive. Water balance Warmer temperatures and higher vapor-pressure deficit mean plants LOSE more water per unit of photosynthesis. Animals face greater dehydration risk; aquatic species face altered hydrology. Food acquisition & reproduction Changed phenology, drought, and heat reduce the resources available for growth and reproduction. Fewer seeds, fewer offspring, lower survival. Examples of species already affected Term Definition Pika Small alpine mammal restricted to cold, rocky talus. Warming pushes them to higher elevations — eventually they 'run out of mountain.' Already extirpated from lower-elevation sites in the Great Basin. Tuatara Reptile with temperature-dependent sex determination. Warming skews sex ratios toward males, threatening population persistence. Wolverine Depends on persistent spring snowpack for denning. Declining snowpack reduces suitable reproductive habitat. 6.2 Responses of species: MOVE, ADAPT, or DIE Move: shift range poleward or upslope to track suitable climate (classic response). Range shifts are highly variable across species — depends on dispersal ability, habitat specificity, and whether barriers (cities, roads, water bodies) intervene. Adapt: through plasticity (phenotypic change within a lifetime) or evolutionary change (genetic change across generations). Long-lived species with small populations adapt slowly. Die: local extirpation or global extinction if neither option is available fast enough. 6.3 Phenology Phenology: The timing of recurring biological events — bud burst, flowering, migration, breeding, hibernation. Climate change is advancing many spring phenological events (earlier bloom, earlier migration). Phenological mismatch occurs when interacting species shift their timing differently — e.g., a migratory bird arrives after its caterpillar prey has already peaked. Mismatches cascade through food webs. 6.4 Characteristics of climate-vulnerable species Narrow thermal tolerance (specialists) Poor dispersal ability (can't move to new climate) Long generation time, low reproductive rate (slow to adapt) Small, fragmented populations (low genetic variation, high stochastic risk) Dependence on climate-sensitive habitats (snowpack, sea ice, coral reefs, alpine tundra) Narrow geographic range, especially on islands or mountain tops (nowhere to go) Tightly tied to a specific phenological window or species interaction 6.5 Why current climate change is especially damaging Rate — change is occurring faster than most species can adapt or move Barriers — human land use has fragmented habitat, blocking the range shifts species used during past climate changes Cumulative stressors — climate change interacts with pollution, invasive species, overharvest, and habitat loss Interconnected systems — ecosystems, human agriculture, and global supply chains are all calibrated to current conditions 6.6 Mitigation vs. Adaptation Term Definition Climate MITIGATION Actions that reduce the magnitude of climate change itself — typically by lowering atmospheric greenhouse gases. Examples: switching to renewables, reforestation (sequestering carbon), reducing fossil-fuel use, more efficient buildings and transport. Climate ADAPTATION Actions that help humans and ecosystems COPE with the climate change that is already happening / unavoidable. Examples: creating migration corridors, building climate-resilient ecosystems through forest thinning, adjusting USDA seed zones, changing crop choices, updating hunting/fishing regulations, designing for sea-level rise. Quick quiz check Planting trees to sequester carbon = MITIGATION (reduces atmospheric CO₂). Thinning Southwest forests to make them more fire-resilient = ADAPTATION (copes with changing fire regime). Geoengineering proposals like stratospheric aerosol injection = a controversial form of mitigation (reduces incoming solar energy). Special cases of adaptation Managed (assisted) relocation: Actively moving species to areas outside their current range that are projected to become climatically suitable. Benefits: may be the only option for species that cannot disperse fast enough; can save species from extinction. Risks: recipient communities may experience novel interactions; potential to create invasive species; ethical questions about intervention. Assisted evolution: Human intervention to increase the rate of evolutionary adaptation — e.g., selective breeding for heat tolerance, or hybridization with warm-adapted populations. Benefits: keeps species in place; works for species that cannot move. Risks: may reduce genetic diversity; unintended consequences; can go wrong (outbreeding depression). 6.7 Corridors, climate refugia, and conservation design Climate refugium: A location whose physical or biological features allow species to persist despite regional climate change — e.g., high-elevation cool pockets, deep canyons, shaded slopes, coastal fog zones. Incorporating corridors (to enable range shifts) and refugia (places species can hold on) into reserve design is essential for climate-integrated conservation. A high-elevation forest that remains cool despite regional warming can serve as a seed source for recolonization — that's the textbook example of a refugium supporting resilience. Final thoughts: making an argument about climate-integrated conservation You should be able to give your own opinion on climate-integrated conservation and defend it. A solid answer acknowledges trade-offs: traditional 'protect what is there' approaches may fail under rapid change, but aggressive interventions (managed relocation, assisted evolution) carry real risks. Most conservation scientists argue for a portfolio approach — protect refugia, build corridors, and use active interventions only where the alternative is extinctionl

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VHS Study Guide Psychology WEEK 1: Psychology as a Science The goal of this week is to distinguish between "Pop Psychology" (myths) and "Empirical Science" (facts). 1. The Philosophical Roots & "Big Names" Wilhelm Wundt: Established the first psychology lab (1879). He used Structuralism, trying to map the "structure" of the mind through Introspection (having subjects report every tiny sensation they felt). Sigmund Freud: Founded Psychoanalysis. He believed behavior is driven by the Unconscious mind and childhood traumas. He used dream analysis and "free association." Behaviorism (Watson & Skinner): They rejected Freud. They argued psychology must be an Empirical Science, meaning we only study what we can see and measure. Watson: Famous for the "Little Albert" study (fear conditioning). Skinner: Focused on how rewards/punishments shape behavior (Operant Conditioning). Ivan Pavlov: A physiologist who discovered Classical Conditioning (associating a neutral stimulus, like a bell, with a natural reflex, like drooling). Maslow’s Hierarchy of Needs: A Humanist theory. It’s a pyramid starting with basic survival (food/water) and moving up to Self-actualization (reaching your full potential). 2. The "Brain Traps" (Critical Thinking & Myths) Word-of-Mouth: We believe things just because we’ve heard them a lot (e.g., "We only use 10% of our brain"—FALSE). Desire for Easy Answers: People prefer a "quick fix" (like a 5-minute cure for anxiety) over complex scientific reality. Selective Perception: We only notice things that confirm our existing beliefs. Post Hoc, Ergo Propter Hoc: "After this, therefore because of this." The logical error of assuming that because Event B followed Event A, Event A must have caused it. Inferring Causation from Correlation: The most common exam trap. Just because two variables move together (like heat and crime), it doesn't mean one causes the other. Reasoning by Representativeness: Stereotyping. Thinking a person "looks like" a certain role, so they must be that role (the "Finance Bro" vest example). WEEK 2: Scientific Inquiry and Research This is the "How-To" of psychology. You need to know the difference between just watching people and running a real experiment. 1. Research Methods Naturalistic Observation: Watching subjects in their natural habitat without interfering. High "real world" accuracy, but you have zero control. Case Study (Clinical): An intensive, detailed look at one unique individual (e.g., a person with a rare brain injury). Great for detail, but you can't apply the results to everyone. Archival Research: Looking at old records, newspapers, or medical files to find patterns. Longitudinal vs. Cross-Sectional: Longitudinal: Following the same group of people for 20+ years. (Expensive, but shows true change). Cross-Sectional: Comparing different ages at the same time (e.g., testing 10-year-olds and 50-year-olds today). 2. The Experimental Design (The "Gold Standard") Inductive vs. Deductive: Inductive: Starting with observations $\rightarrow$ forming a theory (Bottom-up). Deductive: Starting with a theory $\rightarrow$ testing it with an experiment (Top-down). Independent Variable (IV): The variable the researcher manipulates (The "Cause"). Dependent Variable (DV): The variable being measured (The "Effect"). Control vs. Experimental Group: The experimental group gets the "treatment"; the control group gets a placebo or nothing. Random Assignment: Every participant has an equal chance of being in either group. This prevents Bias. Single-Blind vs. Double-Blind: Single: Participants don't know which group they are in. Double: Neither the participants nor the researchers know. This prevents the researcher from accidentally giving "cues." WEEK 3: Biology and Behavior The "Hardware" section. How the physical brain creates the "Pink Slime" experience. 1. The Nervous System Map Central (CNS): Brain and Spinal Cord. Peripheral (PNS): Everything else. Somatic: Voluntary movements (walking). Autonomic: Involuntary (heartbeat). Sympathetic: "Fight or Flight" (Eyes dilate, heart speeds up, digestion stops). Parasympathetic: "Rest and Digest" (Calms the body down). 2. The Neuron (The Building Block) Dendrites: Receive messages. Soma (Cell Body): Process info. Axon: Sends the electrical signal. Myelin Sheath: Fatty tissue that speeds up the signal. Synapse: The tiny gap between neurons where chemicals travel. Neurotransmitters: Agonist: A chemical that mimics a neurotransmitter (enhances the effect). Antagonist: A chemical that blocks a neurotransmitter. 3. Brain Tools & Anatomy EEG: Measures electrical brain waves (good for sleep studies). MRI vs. fMRI: MRI shows structure (a picture); fMRI shows function (where blood is flowing). PET Scan: Uses radioactive "tracer" sugar to see which parts of the brain are active. The Endocrine System: Uses Hormones (slow-acting chemicals) released into the bloodstream by Glands (like the Adrenal or Pituitary). 4. The "Hidden" Biological Details (Week 3) Refractory Period: After a neuron fires, it needs a tiny "recharge" break before it can fire again. Think of it like a camera flash or a toilet flushing—you can't do it twice in a split second. Broca’s Area vs. Wernicke’s Area: * Broca’s: Controls Speech Production (Frontal Lobe). If damaged, you know what you want to say but can't get the words out. Wernicke’s: Controls Language Comprehension (Temporal Lobe). If damaged, you can speak, but it's "word salad"—it makes no sense. WEEK 4: Consciousness Consciousness is your awareness of yourself and your environment. It’s not an "on/off" switch; it’s a spectrum. 1. Processing Levels Conscious Processing: Tasks that require focused attention (e.g., learning a new TikTok dance or solving a math problem). Automatic Processing: Tasks we do "without thinking" once they are learned (e.g., walking or an experienced driver steering a car). 2. Altered States Hypnosis: A state of extreme self-suggestion where a person is highly open to direction. Meditation: A practice of focused attention to achieve mental clarity and emotional calm. Daydreaming: A shift in attention away from the current task toward internal thoughts and "mental movies." 3. Psychoactive Drugs (The "Drug Cabinet") Depressants (Alcohol, Barbiturates): Slow down the Central Nervous System (CNS). They decrease heart rate and reaction time. Stimulants (Caffeine, Nicotine, Cocaine, ADHD meds): Speed up the CNS. They increase heart rate and energy. Opiates (Heroin, Morphine, Vicodin): Specifically target pain receptors. They mimic Endorphins to stop pain and create euphoria. Hallucinogens (LSD, Marijuana, Psilocybin): Distort perceptions and evoke sensory images in the absence of sensory input. WEEK 5: Sleep and Dreams Sleep is a biological necessity, not a luxury. Your brain is incredibly active during this "downtime." 1. Stages of Sleep (The Cycle) Stage 1 (NREM-1): Light sleep. You might experience "hypnagogic sensations" (feeling like you are falling). Stage 2 (NREM-2): Deep relaxation. Characterized by Sleep Spindles (bursts of rapid brain activity). Stage 3 & 4 (NREM-3): Deepest sleep. This is when the body repairs itself. If you wake up here, you’ll feel very groggy. REM (Rapid Eye Movement): The "Dream Stage." Your brain waves look like you are awake, but your motor cortex is blocked—meaning your body is paralyzed so you don't act out your dreams. 2. Dream Theories (Why do we dream?) Freud’s Wish Fulfillment: Dreams are a "safety valve" for unacceptable feelings. Manifest Content: The actual storyline of the dream (e.g., being chased by a giant Pink Slime). Latent Content: The hidden psychological meaning (e.g., you are running away from your final exam stress). Activation-Synthesis: The brain's attempt to make sense of random neural static. The brain "synthesizes" a story from random "activation." Information Processing: Dreams help us sort out the day's events and consolidate memories. Threat Simulation Theory: Dreaming allows us to "practice" surviving dangerous situations in a safe environment. WEEK 6: Thinking and Processing This is about "Cognition"—how we use our "Pink Slime" to solve problems and make decisions. 1. Building Blocks of Thought Concepts: Mental groupings of similar objects (e.g., the concept of "Dogs"). Prototype: The best example of a category. (If I say "Bird," you probably think of a Robin, not a Penguin. The Robin is your prototype). Schemata (Schema): A mental framework that helps us organize and interpret information (e.g., your "School Schema" includes desks, teachers, and bells). 2. Problem-Solving Tactics Trial-and-Error: Trying random solutions until one works. (Slow and inefficient). Algorithms: A step-by-step, logical rule that guarantees a solution. (e.g., a math formula or checking every single aisle in a store to find milk). Heuristics: A mental shortcut or "rule of thumb." It's faster than an algorithm but can lead to errors. (e.g., looking at the signs above the aisles to find the milk). 3. The Biases (Why we make mistakes) Confirmation Bias: Searching for information that supports our preconceptions and ignoring everything else. Hindsight Bias: After an event occurs, believing we "knew it all along." Anchoring Bias: Getting "stuck" on the very first piece of information offered. (e.g., if a shirt is "on sale" for $50 down from $100, you think $50 is a deal, even if the shirt is only worth $10). Availability Heuristic: Estimating the likelihood of events based on how easily they come to mind. (e.g., being afraid of a plane crash because you saw one on the news, even though car crashes are more common). Mental Set: The tendency to approach a problem in one particular way, often a way that has worked in the past but may not work now. WEEK 7: Memory Memory is the persistence of learning over time. 1. The Three Stages of Memory Encoding: Getting information into our brain. Semantic Encoding: Encoding the meaning of words (Deepest processing). Visual Encoding: Encoding images. Acoustic Encoding: Encoding sounds. Storage: Retaining that information. Retrieval: Getting the information back out. 2. Types of Storage Short-Term Memory (STM): Holds about 7 items (plus or minus 2) for about 20 seconds. Long-Term Memory (LTM): Unlimited capacity and can last a lifetime. Explicit (Declarative): Facts and experiences (Semantic = facts; Episodic = your life stories). Implicit (Procedural): Skills (like riding a bike or typing). 3. Memory Sins & Failures Schacter’s Seven Sins: Includes Transience (fading over time), Absent-mindedness (forgetting your keys), and Persistence (unwanted memories that won't go away). Amnesia: Anterograde: You can't form new memories. Retrograde: You can't remember the past. 4. Enhancement Techniques Chunking: Organizing items into familiar, manageable units. Spaced Repetition: Studying small amounts over a long time rather than cramming. Mnemonic Devices: Memory aids like "PEMDAS" for math. 5. The "Subtle" Memory Sins (Week 7) The Serial Position Effect: You are most likely to remember the beginning of a list (Primacy Effect) and the end of a list (Recency Effect), but you’ll probably forget the middle. Pro-Tip: This is why you should study the "middle" weeks (Week 4, 5, 6) extra hard! Misinformation Effect: This is why eyewitness testimony is shaky. If someone asks, "How fast was the car going when it smashed into the pole?" you will remember the car going faster than if they said "hit." WEEK 8: Lifespan Development Developmental psychology examines how we change physically, cognitively, and socially from "womb to tomb." 1. Cognitive Development (Jean Piaget) Piaget believed children think differently than adults and move through four stages: Sensorimotor (0–2 years): Exploring the world through senses. Key milestone: Object Permanence (realizing things still exist even if you can't see them). Preoperational (2–7 years): Symbolic thought (make-believe) but lacks logic. Key trait: Egocentrism (thinking everyone sees the world exactly as they do). Concrete Operational (7–11 years): Logical thinking about physical objects. Key milestone: Conservation (understanding that volume stays the same even if the shape of the glass changes). Formal Operational (12+ years): Abstract reasoning and hypothetical "what if" thinking. 2. Psychosocial Development (Erik Erikson) Erikson focused on "crises" we face at each age. Trust vs. Mistrust (Infancy): Is the world safe? Identity vs. Role Confusion (Adolescence): "Who am I?" (This is the most common exam question). Integrity vs. Despair (Late Adulthood): Looking back on life with satisfaction or regret. 3. Moral Development (Lawrence Kohlberg) Pre-conventional: Doing the right thing to avoid punishment or get a reward. Conventional: Doing the right thing because it's the law or to fit in. Post-conventional: Doing the right thing based on universal ethical principles (even if it breaks the law). 4. Parenting Styles Authoritative: High warmth, high rules. (The "Goldilocks" style—best outcomes). Authoritarian: Low warmth, high rules. ("Because I said so!"). Permissive: High warmth, low rules. (More like a friend than a parent). Uninvolved: Low warmth, low rules. (Neglectful). WEEK 9: Learning Learning is a relatively permanent change in behavior due to experience. 1. Classical Conditioning (Ivan Pavlov) Learning by association (connecting two stimuli). Unconditioned Stimulus (UCS): The natural trigger (Food). Unconditioned Response (UCR): The natural reflex (Drooling for food). Neutral Stimulus (NS): A trigger that means nothing yet (A Bell). Conditioned Stimulus (CS): The bell after it has been paired with food. Conditioned Response (CR): Drooling for the bell alone. 2. Operant Conditioning (B.F. Skinner) Learning by consequences (Rewards and Punishments). Positive Reinforcement: Adding something good to increase behavior (A gold star for working). Negative Reinforcement: Removing something bad to increase behavior (The car stops beeping when you buckle your seatbelt). Positive Punishment: Adding something bad to stop behavior (A speeding ticket). Negative Punishment: Taking away something good to stop behavior (Taking away your phone). 3. Observational Learning (Albert Bandura) Learning by watching others. Famous study: The Bobo Doll Experiment, where kids imitated adults punching a doll. 4. The "Fine Print" of Learning (Week 9) Spontaneous Recovery: After a behavior has been "extinct" (gone away) for a while, it suddenly reappears out of nowhere. (Like Pavlov's dog suddenly drooling at a bell weeks after he stopped). Generalization vs. Discrimination: Generalization: Fearing all dogs because one bit you. Discrimination: Only fearing the specific dog that bit you. WEEK 10: Social Influences This is the study of how the "situation" and "group" overpower the individual. 1. The Stanford Prison Experiment (Zimbardo) Demonstrated the power of Social Roles and Scripts. Ordinary students became abusive "guards" or submissive "prisoners" simply because of the role they were assigned. 2. Influence & Conformity Normative Social Influence: Conforming to fit in and be liked (Dressing like your friends). Informational Social Influence: Conforming because you think the group has more info than you (Following the crowd in a new city). Obedience (Milgram): Following orders from an authority figure, even if it hurts someone else. 3. Group Dynamics Social Loafing: Working less hard in a group than when alone (The "Billy" effect). Deindividuation: Losing self-awareness and self-restraint in a large crowd or behind an anonymous screen. Group Polarization: When group discussion leads to more extreme opinions. Bystander Effect: People are less likely to help if others are around due to a Diffusion of Responsibility. 4. Thinking Patterns Fundamental Attribution Error: Blaming someone's personality for their behavior while ignoring the situation. Cognitive Dissonance: The "icky" feeling when our actions don't match our beliefs (e.g., you hate lying, but you just lied to your mom). We usually change our beliefs to match our actions to feel better. 5. Social Psych "Secret" Terms (Week 10) Self-Serving Bias: When we succeed, we take the credit ("I'm a genius"). When we fail, we blame the situation ("The test was unfair"). Foot-in-the-Door vs. Door-in-the-Face: Foot-in-the-Door: Ask for something tiny first, then the big thing. Door-in-the-Face: Ask for something HUGE (get rejected), then ask for the smaller thing you actually wanted. They are more likely to say yes because it feels like a "compromise." WEEK 11: Multiculturalism & Diversity This is the study of how culture, identity, and group values shape our behavior and how we interact with others. 1. Cultural Values Individualism: Cultures that value personal independence and "Me" goals (e.g., USA). Success is based on personal achievement. Collectivism: Cultures that value group harmony and "We" goals (e.g., Latin America, Asia). Success is based on doing what is best for the family or community. 2. Acculturation (How we adapt to new cultures) Integration: The "Best of Both Worlds." Keeping your original culture while participating in the new one. Assimilation: Giving up your original identity to fully "blend in" with the new culture. Separation: Keeping your original culture and avoiding the new one. Marginalization: Feeling like you don't belong to either culture (The "lonely" state). 3. Metaphors for Society The Melting Pot: The old idea that everyone should blend together and lose their differences to become one "American" identity. The Salad Bowl: The newer idea where cultures live together but stay distinct. You can see the "tomatoes" and the "lettuce"—everyone keeps their unique flavor. 4. Social Barriers Microaggressions: Small, daily slights or "backhanded compliments" toward marginalized groups (e.g., "You’re so articulate for someone from your neighborhood"). Prejudice vs. Discrimination: Prejudice is the thought/feeling (pre-judging), while Discrimination is the action (treating someone differently). WEEK 12: Stress & Health This is the study of how our brain's "appraisal" of the world affects our physical and mental health. 1. The Appraisal Process (Lazarus) Primary Appraisal: Judging if a stressor is a Threat (harmful) or a Challenge (potential for growth). Secondary Appraisal: Evaluating your tools. "Do I have the resources to handle this?" If yes, stress stays low. If no, panic sets in. 2. The Body’s Response (Selye’s GAS) General Adaptation Syndrome (GAS): The three stages of how your body reacts to stress: Alarm: Fight-or-Flight. Heart races, adrenaline hits. Resistance: Staying on "high alert" to cope. This is where you grind through the week. Exhaustion: Your battery dies. Your immune system crashes, and you get sick (The Cohen Cold Study). 3. Types of Stress Eustress: "Good stress." The kind that motivates you to finish a project or perform well in a game. Distress: "Bad stress." Chronic pressure that leads to burnout, fatigue, and health problems. 4. Coping Strategies Problem-Focused Coping: Attacking the problem directly. (Example: Time-Blocking your homework so it isn't overwhelming). Emotion-Focused Coping: Managing the feelings. (Example: Going to the Gym or meditating to stop feeling anxious). 5. Stress "Secret" Terms Cortisol: The primary stress hormone. Great for emergencies, but too much of it "eats" your memory and weakens your heart. Psychoneuroimmunology: The fancy word for the study of how your brain (stress) talks to your immune system. WEEK 13: Mental Wellness & The Science of Happiness The goal of this week is to identify the psychological frameworks and empirical studies that explain how humans build resilience and long-term well-being. 1. The Three Dimensions of Happiness (Module 14.5) According to the textbook, happiness is an enduring state consisting of joy and contentment. It is built through three "lives": The Pleasant Life: Attaining and savoring daily pleasures that add joy to the moment (e.g., the aroma of coffee or the feeling of sunshine). The Good Life: Identifying your unique skills and using them to enrich your life. This is where you find the state of Flow—being so "in the zone" that you lose track of time. The Meaningful Life: Using your talents and efforts in the service of the greater good or to help others, which provides a deeper sense of fulfillment than pleasure alone. 2. The Four Pillars of Well-Being (Wellness Studies) Based on Dr. Richard Davidson’s research, well-being is a "trainable skill" rather than a fixed trait. It is built on: Awareness: Noticing what your mind is doing in the present moment (meta-awareness). Connection: Cultivating kindness and healthy social relationships, which are the #1 predictor of long-term health. Insight: Having curiosity about how your own mind works and not believing every negative thought as a "fact." Purpose: Having a clear sense of direction or a "life compass" that guides your daily actions. 3. Empirical Evidence: The Creswell et al. Study (2014) This study provided scientific proof that mental training has biological effects: The Setup: An experimental design where students were randomly assigned to either a mindfulness group or an analytic control group. The Independent Variable: Brief 3-day mindfulness meditation training (25 mins/day). The Dependent Variable: Biological stress markers (Cortisol levels) and self-reported stress. The Result: The mindfulness group showed significantly lower cortisol levels, proving that meditation fosters biological resilience to stress. 4. Scientifically Proven Benefits of Gratitude Research shows that gratitude is a powerful "reset" for the nervous system: Physical: Improved sleep quality and duration; fewer reported aches and pains. Psychological: Reduces "toxic" emotions (envy, resentment) and increases mental strength. Studies of 9/11 survivors showed gratitude was a major factor in preventing PTSD. Social: Encourages "pro-social" behavior, making people more likely to form and maintain new relationships. 5. Mindfulness vs. Meditation (The State vs. The Practice) It is critical to distinguish between these two often-confused terms: Mindfulness: A state of being. It is the quality of being fully present, aware of where we are and what we’re doing, without being overly reactive or overwhelmed. Meditation: The formal practice or "mental gym" used to train the brain. It is the intentional time set aside to practice techniques that eventually lead to a consistent state of mindfulness. 6. Key Terminology & Cognitive Traps Affective Forecasting: The human tendency to overestimate how much future events (both good and bad) will affect our long-term happiness. We assume milestones like "perfect grades" will provide permanent joy, but they usually don't. Optimism & Resilience: Optimism is the general tendency to expect good outcomes. It is the "engine" of resilience—the ability to "bounce back" from major life stressors (like those listed on the SRRS). Problem-Focused vs. Emotion-Focused Coping: * Problem-Focused: Dealing with the stressor directly (e.g., studying for the test). Emotion-Focused: Managing the feelings associated with the stressor (e.g., taking a nap or exercising)

Chapter 19: Rates, Equilibrium, Spontaneity

MMiPeople Francesco Redi: scientist who tested spontaneous generation with rotting meat and maggot formation with an open container, sealed container, and gauze-covered container, and refuted spontaneous generation Needham: scientist who tested spontaneous generation with boiling chicken broth, sealing the container, and waiting a few days to assess for microbial growth, and supported spontaneous generation Spallanzani: scientist who tested spontaneous generation with further testing, Needham’s experiment, and tested with an open and closed container that was later opened, and refuted spontaneous generation Louis Pasteur: scientist who used swan-neck flasks in his experiment and definitively refuted spontaneous generation Anthony van Leeuwenhoek: scientist who was the first to observe eukaryotic microbes, calling them “wee animalcule” Robert Hooke: coined the term “cell” when looking at cork Matthias Schleiden: observed cells in plant tissue Theodor Schwann: observed cells in animal tissue Rudolf Virchow and Robert Remark: observed cells dividing to make new cells (not mitosis) Hippocrates: suggested disease has natural causes Thucydides: advocated for evidence-based analysis of cause and effect and suggested immunity after observing plague survivors didn't get sick again Marcus Terentius Varro: the first to propose that things we cannot see cause disease Ignaz Semmelweis: physician who observed the spread of disease among patients in different sides of the hospital and instituted hand washing between patients to reduce the spread of disease from patient to patient via healthcare workers Joseph Lister: surgeon who observed post-surgical infection and instituted hand washing and sterilization of medical equipment with 5% phenol solution for less disease Robert Koch: scientist who developed Koch’s postulates to determine the cause of disease and had a rivalry with Louis Pasteur John Snow: questioned the London cholera outbreak and asked questions to the people who had been infected about where they had been and what they had eaten or drank, and noticed that everyone who had cholera used one of two water pumps Classification of microbes What are the 2 domains that are composed of all microbes? Bacteria and Archaea What domain of life is composed only of some microbes? Eukarya What types of microbes do not fit into the domains of life? Viruses and Prions Prions: unicellular organisms in the domains Bacteria and Archaea with no nucleus and have cell walls Viruses: acellular and domainless (not alive) Eukaryotes: unicellular OR multicellular organisms, in domain Eukarya, have a nucleus, have membrane-bound organelles, and include fungi, algae, protazoa, and helminths How many times bigger are bacteria than viruses? 100x A cell is around how many times bigger than an individual bacteria? 10x Cell structures Know the function, general location, and whether they are shared with eukaryotes (if yes similarities/differences) of the following structures: 1. Nucleoid: contains chromosome(s) and nuclear-associated proteins that are usually haploid and circular near the center of the cell, which hold the DNA genetic information without a membrane Eukaryotes = have a nucleus, are diploid and linear Prokaryotes = have nucleoid, are haploid and circular 2. Ribosomes: work with mRNA protein synthesis, made up of proteins and RNA, found in cytoplasm Eukaryotes: 80S, 60 large, 40 small (18S sequencing) Prokaryotes: 70S, 50 large, 30 small (16S sequencing) 3. Cytoplasm: fluid inner layer 4. Fimbriae: short, bristle-like projections for attachment to surfaces 5. Endospores: not all bacteria have, protect bacteria in a dormant state/ harsh environment, found inside bacteria, sporulation = the process of becoming dormant, germination = process of becoming active 6. Plasma membrane: semipermeable, composed of lipids and proteins, controls transport into and out of cell, most inner layer before cytoplasm (ex: facilitated diffusion, active transport, diffusion, endocytosis (Eukaryotes), sterols (Eukaryotes), and cholesterol (Eukaryotes) Same for Eukaryotes 7. Cell wall: protects against harsh changing environments and osmotic stress, contains peptidoglycan in bacteria, contains Gram + and Gram - Steps of Gram stain: dye with crystal violet, iodine (mordant), alcohol (decolorizer), and safranin red If mycobacteria complete an acid-fast stain Gram + has LTA an TA and one membrane Gram - has LPS and 2 membranes 8. Capsule: protective protein shell, outermost layer 9. Pilus: medium projection, adheres to surfaces, does DNA gene transfer 10. Flagellum: long protein projections made of flagellin for movement (ex: 1= monotrichous, one at each end = amphitrichous, many at one end = lophotrichous, many flagella all over the cell = peritrichous 11. Plasmid: circular, double-stranded DNA not part of the chromosome, and can have 1-100 of the same or different plasmids to help with gene transfer, antibiotic resistance, and virulence factors, found anywhere in the cytoplasm Not part of Eukaryotes 12. Inclusion: not all bacteria have, helps with the storage of nutrients and other materials, has protein shell, and is found in cytoplasm (ex: lipid droplets store fats, volutin stores inorganic phosphates, sulfur inclusions store sulfur, gas bubbles store gas for buoyancy in water, magnetosomes store metals for movement) Not part of Eukaryotes; instead, they have vesicles for storage All cellular microbes have what four (4) components? Cell Membrane, Cytoplasm, Ribosomes, and DNA What is the only component of all cells that viruses have? Cytoplasm Know/ be able to identify the shapes of bacteria Round shape: coccus Rod shape: bacillus Vibrio: curved rod shape Short rods with combo of coccus and bacillus: coccobacillus Wavy spiral shape: Spirillum Coiled spiral shape: Spirochete Microbial growth Phases of growth Lag Phase: bacteria gear up for replication by increasing cell size, metabolism, and protein synthesis Log Phase: exponential growth phase, where bacteria actively replicate and are most susceptible to antibiotics Stationary Phase: growth curve flatlines bc bacteria are dying at same rate of growth, begin survival mode and sporulation, produce secondary metabolites, and produce virulence factors, and are low on space, nutrients, and oxygen Death Phase: bacteria die at exponential rate, increase amount of toxic waste, release spores, some spontaneously lyse to feed others, and persister cells refuse to die How do microbes replicate? Through binary fission, fragmentation, budding, and sexually What is a biofilm? Communities of bacteria (steps: colonization, attachment, replication, make EPS with antibiotic resistance, EPS kick bacteria out to replicate somewhere else) How does quorum sensing work? Bacteria want to work together, so they secrete autoinducers, and when you activate enough receptors, they activate a response Growth requirements – classifications and adaptations 1. Oxygen requirements Obligate Aerobes: need O2 to survive Obligate Anaerobes: die in presence of O2 Faculative: mostly need O2 but can survive without it Microaerophiles: need O2 for survival but not atmospheric O2 (low levels) Aerotolerant: can survive with or without oxygen Capnophiles: like high CO2 and low O2 2. pH requirements Acidophiles: low pH (2-4), high H+ environments, efflux pumps to remove H+ ions, changes membrane composition to withstand low pH Neutrophiles: neutral pH (7), found within body Alkaliphiles: basic pH (9-10), modified lipid protein structures, modified electron transport system that use Na+ instead of H+, high OH- environment 3. temperature requirements Psychrophiles: like freezing temperatures a below 0-15 degrees, die at or above 20 degrees, found in cold lakes or the ocean floor, have hydrophobic proteins to increase flexibility, have decreased secondary stabilizing bonds Psychrotolerant: cold not ideal but wont kill them, live between 4-25 degrees (fridge temperature) Mesophiles: moderate temperatures, 20-40 degrees, grow in body Thermophiles: hot environments 50-80 degrees, hot springs, geothermal soil Hyperthermophiles: very hot environments 80-110 degrees, found in hydrothermal vents, increased saturation in membranes, increased stabilizing bonds, alter amino acids to prevent denaturation 4. osmolarity requirements Hypertonic: more water out Hypotonic: more water in Isotonic: equal water in and out Halotolerant: dont require salt but can grow in high salt environments Halophiles: love salt, found in ocean and salt lakes, have increased cytoplasmic glycerol, have efflux pumps for salt 5. barometric requirements Barophile: survive high atmospheric environments like the bottom of the ocean (something at top of mountain has low atmospheric pressure) Microbial Metabolism Means of generating energy (do the processes require oxygen?, which gives the most energy?) Glycolysis: does not require O2 bc it can be used during fermentation, used 2 ATP, makes 4 ATP, NET 2 ATP Kreb’s cycle: requires O2; NET after 1 round= 1ATP, 1 NADH, 1FADH2 (x2 for second round) Electron transport: requires O2, biggest payout of ATP with NET 34 ATP Photosynthesis: does not require O2 as it is a waste product, can do oxygenic and anoxygenic Microbial genetics DNA Replication – enzymes and functions DNA gyrase: unwinds DNA (enzyme) Helicase: unzips DNA (enzyme) Single-stranded binding proteins: bind to DNA so doesnt close back up (protein) Single-stranded binding proteins: bind to DNA so doesnt close back up (protein) DNA polymerase III: lay down new DNA nucleotides, synthesizes leading and lagging strands 5’ →3’(enzyme) DNA polymerase I: removes RNA primers (enzyme) DNA Ligase: seals RNA primers (enzyme) Topoisomerase 4: separates 2 circular chromosomes Transcription and translation – enzymes and function 1. RNA polymerase: turns DNA→ mRNA (transcription) 2. Ribosomes: 30S small, 50S large, 70S total 3. tRNA: A,P, and E sites, bacteria links transcription and translation bc no nucleus, has anticodon at opposite long 3’ end, high energy bond, same active translation process as Eukaryotes Be able to do DNA base pairing, transcription, and translation (given codon table) Also know differences between prokaryotic and eukaryotic Replication, transcription, and translation Genetic Diversity – how does this work? 1. Transformation: uptake of plasmid into different bacteria and is incorporated into its genetic material 2. Transduction: bacteriophage inserts its plasmid into a bacteria (virus that infects a bacteria) 3. Conjugation: like plasmid transfer (ex: rolling circle replication), “bacterial sex” 4

# SSUSH 1–19 Study Guide (Quizlet Style) ## SSUSH 1–5: Colonization, Revolution, and Constitution Southern Colonies - Established mainly to create wealth for England - Economy based on cash crops like tobacco and rice - Used enslaved labor New England Colonies - Founded mostly for religious freedom - Economy based on trade, fishing, and shipbuilding - Small farms and towns Trans-Atlantic Trade - Trade network between Europe, Africa, and the Americas - Included enslaved Africans and cash crops - Helped colonies grow wealthy Mercantilism - Economic system where colonies existed to benefit the mother country - Colonies sent raw materials to England - England sold finished goods back Intolerable Acts - Laws passed by Britain after Boston Tea Party - Punished Massachusetts - Increased colonial anger toward Britain Declaration of Independence - Written mainly by Thomas Jefferson - Declared independence from Britain - Said people can overthrow abusive governments Three-Fifths Compromise - Enslaved persons counted as 3/5 of a person for representation - Increased Southern power in Congress Shays’ Rebellion - Farmer rebellion in Massachusetts - Showed Articles of Confederation was too weak - Led to calls for stronger central government Thomas Paine / Common Sense - Argued independence was necessary - Convinced many colonists war was unavoidable Treaty of Paris (1783) - Ended Revolutionary War - Britain recognized U.S. independence - Made future U.S. expansion possible Federalists vs Anti-Federalists - Federalists wanted stronger central government - Anti-Federalists feared too much national power - Debate led to Bill of Rights Standing Army Debate - Federalists wanted army for defense - Anti-Federalists feared army could threaten liberty --- ## SSUSH 6–10: New Nation, Sectionalism, Civil War, Reconstruction Election of 1800 - Thomas Jefferson defeated John Adams - Criticism of Sedition Act hurt Federalists - Peaceful transfer of power Sedition Act - Made criticism of government illegal - Hurt Federalists politically Marbury v. Madison - Established judicial review - Supreme Court can declare laws unconstitutional Monroe Doctrine - Warned Europe to stay out of Western Hemisphere - U.S. opposed new colonization in the Americas Louisiana Purchase - Bought from France in 1803 - Doubled size of U.S. - Opened West to settlement Second Great Awakening - Religious revival movement - Inspired reform movements Reform Movements - Abolition - Women’s rights - Education reform - Temperance - Goal: improve society James K. Polk - Expanded U.S. territory - Annexed Texas - Settled Oregon boundary - Won Mexican Cession Sectionalism - Differences between North and South increased - North = industry - South = agriculture/slavery Civil War North Advantages - More railroads - More factories - Larger population Civil War South Advantages - Better military leaders - Fought defensive war Lincoln’s Second Inaugural Address - Focused on healing the nation - Called for unity after Civil War Freedmen’s Bureau - Helped formerly enslaved people - Provided food, education, and aid Reconstruction Amendments - 13th: ended slavery - 14th: citizenship and equal protection - 15th: voting rights for Black men --- ## SSUSH 11–19: Industrialization to World War II Railroad Expansion - Helped settle the West - Increased trade and movement - Led to conflict with American Indians Plains Indians - Resisted westward expansion - Forced onto reservations by U.S. government Transcontinental Railroad - Connected East and West - Built heavily by immigrants Ellis Island - Immigration station in New York - Processed many European immigrants Standard Oil / John D. Rockefeller - Used horizontal integration - Bought smaller companies - Created monopoly Labor Unions - Formed because of long hours, low wages, unsafe conditions - Fought for workers’ rights Plessy v. Ferguson - Established “separate but equal” - Allowed segregation and Jim Crow laws World War I Causes - Militarism - Alliances - Imperialism - Nationalism Unrestricted Submarine Warfare - German U-boats attacked ships - Helped cause U.S. entry into WWI Harlem Renaissance - African American cultural movement in 1920s - Literature, music, art flourished 19th Amendment - Gave women the right to vote Great Depression - Began with stock market crash in 1929 - Massive unemployment and poverty Eugene V. Debs - Criticized U.S. involvement in WWI - Punished under Espionage Act New Deal - Roosevelt’s programs to fight Depression - Relief, Recovery, Reform Second New Deal - Focused on long-term reform - Included Social Security Act Social Security Act - Helped elderly, unemployed, disabled - Long-term economic reform Dust Bowl - Caused by drought + poor farming practices - Forced migration west Manhattan Project - Secret U.S

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