BIOL 1108 Notes - MSH Unit 1 (PDF)

BIOL 1108 Notes for 08/16/24: Unit 1: Mount St. Helens (Recovery) 1. Questions: a. How has the ecosystem changed? b. What will affect the order or reestablishment? c. How long will recovery take? Important Definitio...

BIOL 1108 Notes for 08/16/24: Unit 1: Mount St. Helens (Recovery) 1. Questions: a. How has the ecosystem changed? b. What will affect the order or reestablishment? c. How long will recovery take? Important Definitions of Scale: - Species: no “one” definition (can be very general yet defines whether organisms can reproduce with one another) - Population: All of the individuals of a SINGLE SPECIES that interact - Community: All of the populations of LIVING things that interact in a place - Ecosystem: A biological community of interacting organisms and their physical environment/non - living things (BIOTIC and ABIOTIC components) Abiotic Components - Climatic Variables: - Soil (water levels, pH levels, richness of the soil (nutrient composition), soil composition (what soil is composed of) - Amount of sunlight (affected by latitude or weather) - Temperature/weather - Humidity - Amount of Rain Climate: averages and seasonality Abiotic Components - Geological Variables: - Topography: land (whether it is hilly) - Bedrock - Water - Salinity - Dissolved Oxygen Levels - Pollution/Contamination - pH levels - Soils Abiotic Components - Disturbance Variables: - Natural or Human - Scale - Frequency - Intensity - Natural can be such as wildfires, volcanoes, monsoons, tornadoes, diseases, overgrazing, tsunamis - Human can be such as man - made wildfires, urbanization, spread of diseases, hunting, pollution, deforestation, agriculture Biotic Components (Organisms): - Population Size - Population Diversity (Biodiversity) - Growth Rate - Species’ Interactions - Biomass (NPP or Net Primary Production) - Invasive or Keystone Species Scale: - No defined size of an “ecosystem” - No boundaries (mostly) Background Notes: Mount St. Helens Washington State Part of the Cascade Mountains Temperate Rainforest Biome Pacific NW Climate ○ Mild and wet year round ○ Infrequent fire ○ Proximity to ocean - fairly close ○ No snow ○ Very infrequent volcanic events Mountains Characteristics: ○ What abiotic changes happen as you go up in elevation? Temperature decreases ○ What happens to humidity as you go up in elevation? Humidity and rainfall increases ○ What happens to soil as you go up in elevation? Soil can’t support as much biomass, more thinner ○ Air pressure decreases as you go up in elevation (however O2 only changes at REALLY high elevations)  BIOL 1108 Notes for 08/19/24: Unit 1: Mount St. Helens (Recovery) How has the ecosystem changed? Look at how temp, precip, o2, soils, and pressure (abiotic characteristics) change as the elevation increases and decreases. How does elevation impact biotic characteristics? - Changes in biomes because of temperature and precipitation - Biodiversity changes (depends on the scale and perspective) - biodiversity (for now) is the various types of species that are present - When elevation increases, there is usually less biodiversity, but it depends on the regions and plots that are being compared. Therefore, perspective is very important. Mountains: - What is the relationship between the ecosystems or biomes across elevations and across latitudes? - As we increase latitude, you experience the same biotic changes as if you were to go up in elevation. - Increasing elevation changes = increase latitude changes - Mountains changes faster - elevation is changed faster than in latitude (hiking up has faster changes than hiking north) MSH: The Before Times - “Old Growth” forest - never been logged - doesn’t mean “undisturbed” - Diverse forests and lots of wildlife - “Rich” soil - lots of available nutrients for plant growth - Temperate Rainforest Biome - Not a homogenous ecosystem (lots of changes and dif ecosystems based on elevation) May 18th, 1980 - 8:32AM At Mount St. Helens, only the North slope was affected so in this natural experiment, the South slope could be used as the natural control to view and compare the recovering ecosystems. - Pyroclastic Flow/Pumice Plain: directly everything became like a moon crater - no life - most impact, moonscape, nothing alive - Everything covered with up to 6’ of tephra/ash - Tephra (Ash) - rock dust (Ash is result of fire, yet tephra is simply rock dust not directly result of fire) - Blow Down Zone/Lateral Blast: anything above ground in this area was immediately killed, but ones underneath could have survived such as fungi and rodents and seeds and bacteria (it recovered fairly quick) - trees snapped off at ground, large area - Scorch Zone: furthest affected area from region, had things surviving because anything below the snow line allowed for survival (snow helped insulate organisms)  What will affect the order of reestablishment? *What can REACH the area (pumice plain) first? **The first to REESTABLISH will need to be the first that can REACH & SURVIVE - Animal Migration - What animals do you think will reach the pumice plain first (based on migration rates)?? - Rodents - Birds - Large Animals - Insects Migration Rates: (look over migration graphs) - Based on question prior: - Plants are generally among the slowest organisms to migrate. - Rate of animal REESTABLISHMENT is based on plants - Plant Dispersal - Seed Dispersal - How seeds/spores are spread away from the parent plant Why do plants spend energy to disperse seeds? - Avoid offspring competing with parents for resources (no offspring competing with each other either) Ways of seed dispersal: - Wind - very long distance yet random landing based on chance (lightweight would be carried only) - Animal (fruit) - long distance, takes energy - Animal (sticky) - long distance, needs hardware - Animal defecation - Gravity - short distance, rolls downhill (low energy) - Through animals’ fur - LOTS of ways (such as water and etc)  BIOL 1108 Notes for 08/21/24: Unit 1: Mount St. Helens (Recovery) Nesting mourning dove outside the mlc steps Trial gardens: impatiens - just starting to set seed with exploding seed pods Catch - Up from Last Time Notes: - Seed dispersal - how plants migrate from gen to gen - Different dispersal strategies have pros and cons - Wind - Fruit for animals - Ballistic/gravity - Sticky seeds Ability to REACH -> Long distance dispersal - What seed characteristics increase dispersal distance? Weight Size What is a seed? ➔ Anatomy of a Seed: ◆ Seed Coat: Is like the embryo sack wall – offers protection from environment From getting crushed, digested, dried out, waterlogged, etc. Thick or thin Why aren’t they all thick? ○ Energy. Why use energy to be extra and quirky?? ◆ Plumule: Becomes the shoot ◆ Hypocotyl: Becomes the stem ◆ Radicle: Becomes the root ◆ Cotyledon: Becomes the food storage Food (energy) (egg yolk of seed) Storage as fats and oils for growing baby plant ○ Large (acorns, avocadoes) and small (sesame, poppy) ○ Peanut butter is made up of just cotyledon ➔ Pros of having a Large Cotyledon: ◆ Can store more energy ◆ Can last longer before sprouting (germination) ◆ Can grow quickly to overtop competitors before they need to tap into their own food and water ◆ Each seed is individually more likely to survive ➔ Advantages of Small Cotyledon and Seed Coat: ◆ Can produce many more ◆ Longer distance dispersal ◆ Each seed has a lower chance of survival (per capita survivorship) ➔ Evolutionary Trade - offs: ◆ A pool of energy can be allocated in different ways  ◆ Advantages and disadvantages of each selection ◆ Impossible to have the best of both worlds ◆ Traits that help a seed reach first, reduce survival probability ◆ Traits that help survival probability, reduce dispersal distance ➔ Fitness refers to the parent ◆ Number of offspring that survive to reproduce ◆ How much an individual contributes to the next generation ◆ Both sizes of cotyledon have equal fitness What else determines survival? 1. Large seeds 2. Ability acquire nutrients once the cotyledon runs out, after germination a. Germination = seed emergence b. Seed to seedling What nutrients do seedlings/plants need? Structural nutrients: Carbon ○ Plants get this from air Hydrogen ○ Plants get this from water exclusively the roots through soil NOT air Oxygen ○ Plants get this from air and soil and photosynthetic product Primary nutrients: (get through fertilizer) Nitrogen - for green foliage Phosphorous - for roots and blooms Potassium - for overall plant health When you buy fertilizer, check out the NPK numbers and match it to the problems you're having with your plants or what you're growing Macronutrients: (NPK Fertilizer) Needed in large quantities to make nucleic acids Micronutrients: Needed in small quantities  BIOL 1108 Notes for 08/23/24: Unit 1: Mount St. Helens (Recovery) What do plants need these nutrients for? C, H, O: (carbohydrates/sugars) ○ Cellulose - wood and stems ○ Glucose Metabolism [cellular respiration] N: ○ DNA (nitrogenous bases) Adenine Thymine Guanine Cytosine ○ Proteins (including enzymes) P: ○ DNA - phosphate backbone A little bit of a lot of other nutrients (micronutrients) ○ Magnesium (&N) - chlorophyll ○ Magnesium is used to trap sunlight ____________________________________________________________________________ **Lupines are the first plant that was reestablished in Mount St. Helens - Lupines are known to be early establishers Hypotheses of why lupines are able to survive: 1. Lupine were the first plants to establish in the pumice plains, despite being poor dispersers, because they are the only ones able to survive in the volcanic ash. 2. Pearly Everlasting and Fireweed can survive in the pumice plain’s tephra, but didn’t reach the pumice plain first. What we actually found: - Fireweed and other plant seeds DID REACH the interior of the pumice plain quickly, but could not SURVIVE there. - Lupine were the only plants that could SURVIVE (took them 2 years to reach) ____________________________________________________________________________ What happens if organisms don’t get what they need? Living Resources: - Liebig’s Law of Minimum - Individuals: - Individuals will grow only up to the point it runs out of a vital resource, even if there are surpluses in other categories - Populations: - Populations will grow only up to the point they run out of a vital resource. - **Similar to limiting reactants in chemistry ➔ Indeterminate Growth:  ◆ No maximum size, or are at a size where there are not limits on a size (ex: goldfish) - only works sometimes Limiting Resources: - Liebig’s Law of the Minimum - Important assumptions for this concept: - Only one limiting resource at a time (one has to be the lowest) but it is possible that it changes over time - Too much of a nutrient is not harmful - Ignore the realistic size limitations for organisms **AI predicted protein structures - Critical Assessment of Protein Structure Predictions (DeepMind)  BIOL 1108 Notes for 08/26/24: Unit 1: Mount St. Helens (Recovery) How do plants obtain N? - Through their roots - There were trace amounts of nitrogen within MSH Tephra (nitrate and ammonium was missing) There was no organic C within MSH tephra but that is okay because plants get C through air/oxygen. Why do organisms need N? Proteins - macromolecules with MANY functions ○ Muscles, cellular communications, enzymes, and more ○ Proteins are made up amino acids DNA - nitrogenous bases (ACTG) Chlorophyll Neurotransmitters Proteins Overview: 1. Complex molecules made of amino acids that do many things 2. Synthesized (made) using ribosomes and an mRNA template (translation) 3. Can denature (change shape) and can occur when too hot (temperature) and pH can also denature Amino acids join together to make proteins (DNA codon → mRNA → tRNA → amino acid → protein (AA chain - primary structure) Structures: Primary (amino acid chain) Secondary structure (alpha helix and beta helix) Tertiary Structure (polypeptide chain) Quaternary structure (assemble subunits) ** A change at any stage affects “downstream” folding ** DNA Mutation → new AA sequence (primary structure) ** New order → new shape → new function and number Amino Acid Structure: ➔ Contains: ◆ R group ◆ Amino group ◆ Carboxyl group ➔ Primary structure: ◆ Peptide bonds: C-N covalent bond ➔ Secondary structure: ◆ Coils or crimps ◆ Hydrogen bonds are responsible (ONLY) Not related to r groups, only backbone and partial charges ➔ Tertiary Structure:  ◆ Specific 3D structure R - groups determine tertiary structure IMFs, ionic bonds, and sometimes disulfide bridges determine exact folding pattern Disulfide bridges: covalent S - S bonds (cysteine only) ➔ Quaternary Structure: ◆ Multiple tertiary subunits bound together ◆ Same interactions as tertieeeary Basic Chemistry Review: Bonds and IMFs - Molecule Structure ➔ Bonds - “permanent” connections between atoms in a single molecule (INTRAmolecular forces) ◆ Covalent (share electrons) ◆ Ionic (donate/steal(accept) electrons) ➔ IMFs - Intermolecular Forces - electrostatic (charge) attractions between molecules that can vary in permanence and strength ➔ Electronegativity - how tightly an atom holds onto its electrons (F is most EN) Bond EN: Determined by electronegativity Covalent bonds (from 0-.4) - share electrons When electrons EN difference is over.4 threshold and reaching 1.7, electrons are known as being donated so then is considered Ionic bonds ➔ Type of bond is based on the relative amount of time electrons spend around involved atoms ➔ Time depends on the differences in electronegativity ➔ Once two atoms are considered ionic, one atom that receives more charge has one whole complete charge rather than being called partial like in covalent Types of Bonds: Ionic Bond - permanent attractions between 2 ions (whole charged atoms) ○ Anions - neg charge (extra electrons) ○ Cations - pos charge (missing electrons) Ex: NaCl Sodium donates an electron to chlorine, so sodium now has a full positive charge while chlorine has full negative charge Covalent Bond - atoms share a pair of electrons ○ Codependency (low energy state) holds them together ○ Double or triple bonds are possible (such as N2) Ex: HCl Covalent bonds are very stable Bond Polarity: Non - polar bonds - mostly even distribution of shared electrons ○ Difference in electronegativity is ≤ 0.4 Polar Bonds - electrons are not shared evenly (ionic and some covalent)  ○ Difference in electronegativity > 0.4 Covalent Bond Polarity ○ If difference is ≤ 0.4, no partial charge (non polar covalent) ○ > 0.4: unequal distribution of e- → partial negative (δ −) and partial positive (δ+) charges within a molecule ○ Noted with (δ) delta ○ One atom with higher electronegativity will have positive charge IMFs (non covalent interactions) 1. Dipole - dipole: an attractive force between any partial positive charge in one molecule and the partial negative in another molecule 2. Hydrogen “bond” (should not be considered bond, but rather a force): a special dipole - dipole between a partial positive δ+ H and an O, N, or F with a partial negative in another molecule a. 3 Part​​Test: Hydrogen Bonds i. Is it between molecules ii. Is there a partially positive H iii. Is it connected to a partially negative something else iv. **Then yes! It is a H bond, no other complications 3. Non - polar interactions: weakest IMFs between non charged atoms a. Ex: London Dispersion and Hydrophobic Attractions, dipole induced dipole attractions 4. Shape is determined by bonds and IMFs Proteins: With oxygen and nitrogen involved in a bond, it is most likely a polar bond - Therefore, peptide bonds are polar bonds Structure Review: - Primary: Straight AA chain (peptide bonds) - Secondary: crimped (beta) or curled (alpha helix) - h bonds - Tertiary - Quaternary AA Groups: ➔ (-) charge ◆ Aspartic Acid ◆ Glutamic Acid ➔ (+) charge ◆ Lysine ◆ Arginine ◆ Histidine ➔ Polar (partial charged regions) ◆ Serine ◆ Threonine  ◆ Tryosine ◆ Asparagine ◆ Glutamine ➔ Non Polar (no charged regions) - Not charged because there are no reactive molecules such as Oxygen linked to CH groups ◆ Valine ◆ Cysteine ◆ Proline  BIOL 1108 Notes for 08/28/24: Unit 1: Mount St. Helens (Recovery) **N^2 has a TRIPLE covalent bond (available everywhere but not accessible to everything) Nitrogen Cycle: 1. Assimilation: plants take up nitrate (NO3) from the soil i. How does N get there? 1. Through the roots b. Soil Bacteria convert Ammonium into Nitrite and Nitrate i. How do we/animals get the N we need? 1. We eat things, we obtain our nitrogen by eating it 2. Nitrogen Fixation: a. Converts N2 → NH4 (eventually NO3) b. Only done by very few bacteria c. Lightning - first bacteria used lightning to aid them in nitrogen fixation most likely 3. Some plants (mostly legumes) have managed to harness N - fixing bacteria to provide their own supply of NO3 a. Nitrogen fixing bacteria (N-fixers): i. Plants are not nitrogen fixers, the bacteria are ii. **LUPINES ARE LEGUMES  1. Lupines can live in soil without nitrogen and still simply produce their own nitrogen Why don’t all plants just host N - fixing bacteria? ENERGY!! (if you don’t need it, don’t do it!) Plants without Nitrogen fixing bacteria have more energy for: - More seeds - Growing fast - More roots - Etc. How does protein folding relate back to Mount St. Helens? The lack of nitrogen in MSH soil led to a lack of proteins being made, which was interesting because lupine was still able to survive.  BIOL 1108 Notes for 08/30/24: Unit 1: Mount St. Helens (Recovery) - Remember: Lupines are legumes, which are hosts to nitrogen - fixing bacteria and able to aid the plant survive in nitrate lacking soil. - Due: Podcast tonight Nitrogen Fixing Bacteria (cont:) Mutualistic vs. Symbiotic Relationships: ➔ Mutualism: both species benefit from this interaction ➔ Symbiotic: Live their lives in close physical proximity (together/touching) and evolved together (gray area) Symbiosis: ➔ Any relationship where two or more species live closely together Commensalism: ➔ Some types of dispersal work under this. Herbivory: (ex: moose eating plants) Competition: ➔ Intra - specific Competition ◆ Between individuals of the same species ➔ Inter - specific Competition ◆ Between individuals of different species - Both become -/- because they are both suppressing each other as populations - Ex: lions and leopards all feasting on gazelle population - If lions are gone, leopard population goes up and vice versa may also occur so if both present, they’re suppressing each other’s population size so both become -/- Altruism: ➔ One organism acts to increase the fitness of another organism at a cost to itself (decreasing fitness) ◆ Ex: Animal best friend stories Kin Selection: ➔ Often mistaken for altruism - an organism increases the fitness of a relative at a cost to its own (ants and bees (queen bees)). Mathematically proven (to be mutualistic) Facilitation: ➔ When one organism changes the environment, leading to its own eventual replacement. (delayed/accidental altruism?? Hurts subsequent gens)  Species Interaction Matrix Other organisms - x-axis Itself - y axis + - 0 Herbivory + Mutualism Parasitism Commensalism Predation Altruism - Facilitation Competition Very unlucky? 0 Lucky? Unlucky? No interaction MSH LINK: Lupine allowed for facilitation. Throughout lupine’s life, it was using nitrogen - fixing bacteria continuously. When lupine died, it decomposed and turned into soil where traces of nitrogen were starting to be found within the pumice plain. Therefore, over several generations, more and more nitrogen allowed for more species to return back to the pumice plain because they can start to truly survive within the nitrogen filled soil. Facilitation Examples: How do plants facilitate each other’s growth? Increased soil moisture (plants that create shade help create soil moisture) Soil Building - decay/wind Temperature/Humidity Regulation Attracting pollinators Nitrogen Fixing Bacteria (hosting useful organisms)  BIOL 1108 Notes for 09/04/24: Unit 1: Mount St. Helens (Recovery) Succession: ➔ The process of development that over time, gradually and predictably changes the biological community ➔ Species progression: pioneer stages (facilitation occurs) → intermediate stages → climax community ◆ Bare rock → lichens → small annual plants, moss → perennial herbs, grasses → shrubs, shade - intolerant trees → shade - tolerant trees ◆ ➔ Climax community: the stage that will persist as a static ecosystem and will continuously regenerate itself (until a disturbance) **Succession on MSH: ❖ Lupine was apart of pioneer species and so was eventually fireweed, pearly everlasting ❖ Willows, red alder were in intermediate stages (early successional forest) - will not really be able to regenerate but will be eventually replaced by shade - tolerant trees ❖ Noble fir, douglas fir, red cedar were apart of climax community (late successional forest) **Not every successional pathway is the same. Random variation can lead to very different outcomes. Changes in Soil Development: Soil ends up increasing in number of nutrients and amount of carbon it can hold over time Primary v Secondary Succession: SAME idea, just DIF starting point - Primary: starting from bare rock - Secondary: starting with at least some soil Where do we find primary succession? - Mountain Tops  - Glacial Retreat - Parking lots **The pumice plain experiences secondary succession, because it has soil, but it isn’t good soil. Yet, we skip the lichens and moss, we have more soil rather than bare rock. Complexity in Succession: Types of Complexity: ➔ Structural Complexity ◆ Vertical (how layered something is from bottom to top) Layers of a Forest ○ Canopy ○ Sub - Canopy ○ Understory/shrub layer ○ Forest floor ○ Soil ◆ Horizontal (patchiness) Imagine looking down from above - which has more heterogeneity or diversity ➔ Soil Complexity ➔ Biodiversity Disturbance can affect the path to succession and make succession go the other way - Disturbance acts in opposition to succession - Disturbance allows succession to be constantly occurring at different stages and scales - forming patches (leads to horizontal complexity!) Succession and disturbances are always assumed to be happening in natural ecosystems ➔ That means vertical complexity and horizontal complexity are constantly increasing, at least until a large, catastrophic disturbance (like a volcanic eruption) happens - can reset the system Ways to Study for BIOL Test: ➔ Concept Maps ◆ For large topics, individual lectures or whole unit ◆ Draw with partner and talk about new connections ◆ Start with big ideas, then gradually add more details ➔ Word Salad ◆ Put all concepts or vocab words on slips of paper in hat - pull out 2 and describe how both related ➔ Rewrite review quiz questions ➔ Write out why each answer in WRQ is right of wrong, writing helps clarify thinking ➔ Think of new/imaginary examples for concepts In Class Quiz: - Overall, the South Slope has high horizontal complexity. Some patches have either low or high vertical complexity depending on successional age. **Causes of Structural Complexity: - Vertical complexity: succession - Horizontal complexity: disturbance - However, both will increase over time. Disturbance acts in opposition to succession. Disturbance allows for horizontal complexity.  BIOL 1108 Notes for 09/06/24: Unit 1: Mount St. Helens (Recovery) Disturbances: ➔ The size (scale), type, and frequency (how often) of disturbances affect the ecosystems differently. (described in ecosystem def) **Succession and disturbance together over time create an ecosystem in dynamic equilibrium. - like in forest ecosystems Dynamic equilibrium - an ecosystem in a constant state of change/flux (due to disturbance and succession) Develops over long periods of time, not quickly after major disruption Contains patches in different successional stages ○ Climax community and dynamic equilibrium are not the same Biodiversity: ➔ For now, how many kinds of organisms are in a place ➔ ↑ diverse habitats, ↑ organisms Why are some places more biodiverse than others? - Time/age - succession and dynamic equilibrium - Ecosystem complexity - horizontal/vertical Besides biological reasons, why do we care about biodiversity? Ecosystems needed for food Moral responsibility to protect organisms Tourism Emotional connections to organisms ○ Cute, dumb pandas! So fluffy! Why do we care? How much would it cost to provide all of these ecosystem services for ourselves? ➔ Carbon sequestration ➔ Pharmaceuticals ➔ Coastal Hurricane Protection ➔ Erosion Control Biodiversity Calculation Video: There are practice problems on eLC. Watch the biodiversity calculations video. You will need a non - graphing calculator even for exam. Simpson’s Biodiversity Index! Resistance - ability to prevent impacts from disturbance - Ecosystems with high biodiversity change less Resilience - ability to recover after a disturbance - Ecosystems with high biodiversity recover faster Stability - Resistance and resilience contribute to fewer fluctuations in an ecosystem - Allows for more complexity of ecosystem by allowing for more organisms to come in an evolve Ecosystem Stability: ↑ Complexity leads to ↑ Diversity leads to ↑ Stability (Just like genetic diversity is advantage in a population, so too is ecosystem complexity) The same relationship can also work in reverse. Loss of biodiversity decreases stability and lowers complexity and lowered complexity leads to lower biodiversity. - The more biodiversity, the less disturbance experienced Forest gaps: ➔ When a gap opens, there is a race to capture that space. ➔ Canopy gap allows for trees to: ◆ Goal: reach canopy to increase fitness ◆ Have multiple short term and long term strategies ◆ Evolutionary tradeoffs ➔ Traits of early successional trees: ◆ The first species to come in and establish in a place with high light High max growth rate Low persistence Low shade tolerance Low longevity ➔ Traits of late successional trees: ◆ Can establish underneath an existing canopy; they slowly make their way to the canopy themselves Low max growth rate High persistence High shade tolerance High longevity ➔ Traits involved with Trees: ◆ Maximum growth rate: How fast a tree is able to grow given ideal conditions ◆ Persistence: How little growth a tree can sustain without dying ◆ Shade Tolerance: How much light a tree requires in order to live ◆ Longevity: Max life span