Notes: -Lectures 1-4, 8, and 29 are NOT on the Final.

As such, theyre not here either -About the numbering: a number is a concept; CS means case study; P means process; T means table. -Lecture 17 is at the end for reasons I dont feel like typing out -I did not include any information on problem set calculations (population problems, trophic level problems, index calculations, BEES, or LCA) -The C, N, and P cycle are at the end -I did not include the dates from Space and Time lecture. Theyre on Blackboard -I apologize for any grammar/spelling mistakes and incompleteness. Remember, these are my personal notes. Use them at your own risk.

Urban Engineering Ecology Summary

1- Organism: any living system made up of cells that has a metabolism, grows, reproduces, dies, and responds to its environment. 2- Prokaryotic cell: simple type of cell with no nucleus. Its genetic material just oats in plasma. 3- Eukaryotic cell: has organelles and a nucleus. 4- Carbohydrates: molecules made up of Carbon (C), Oxygen (O), and Hydrogen (H). They can provide energy, like glucose and starch do, or they can provide structure, like cellulose. 5- Amino acids: molecules made up of C, H, O, and Nitrogen (N). They are the basic building blocks of proteins 6- Lipids: molecules made of C, H, and O that are arranged in long chains. They provide energy, and are part of cell membranes. 7- Saturated lipid: all carbons within the lipid have single bonds only. 8- Unsaturated Lipid: has carbons that have double bonds. 9- Nucleic Acids: molecule that carries our genetic material. 10- RNA: single strand of genetic material. It has oxygen in its composition. 11- DNA: double strand of genetic material. It does not have oxygen in its structure.

12- Nitrogenous bases: molecules made up of Phosphorous (P), sugar, and one or two rings. They are Adenine, Thymine (exclusive to DNA), Guanine, Cytosine, and Uracil (exclusive to RNA). They each have complementary pairs (A-T, G-C, and A-U). 13- Messenger RNA (M-RNA): molecule that copies information from the DNA and takes it to the ribosome. 14- Ribosome: organelle in the cell that receives and reads the genetic information from the messenger RNA. 15- Transfer RNA (T-RNA): works together with the ribosome. it provides the amino acids that build proteins. P1- How DNA Produces Proteins: The DNA gets unzipped and an M-RNA copies the bases from the DNA with complementary bases. These bases are taken to the ribosome where they are read. Every three nitrogenous bases that the ribosome reads from the information the messenger RNA brings, corresponds to an amino acid that a T-RNA brings and adds to an ever growing chain of amino acids that will eventually be a protein when the chain gets long enough. 16- Photosynthesis: metabolic process by which a plant takes carbon dioxide and water to produce glucose and oxygen. 17- Respiration: catabolic process through which an organism breaks the carbon bonds in glucose by using oxygen to produce carbon dioxide, water, and energy. 18- Glycolysis: less efcient form of acquiring energy that is used when little or no oxygen is available (such as when you exercise). Glucose has its carbon bonds partially broken to produce a little bit of energy and two pyruvates (3 carbon atoms) which later decompose into lactic acid. 19- Mitosis: process by which a cell replicates 20- Meiosis: process by which sexual cells replicate P2- How Mitosis Works: The cell has its DNA replicated to get two copies of it in the same cell. Both copies move to opposite sides of the cell, and the separation begins. The end product is two cells with identical properties. P3- How Meiosis Works: one male and one female cell combine to form a single cell which has 46 pairs of chromosomes. The cell divides twice recombining the material randomly to get four daughter cells with 23 pairs of chromosomes. 21- Allele: form of a gene or group of genes. One is provided by each parent and between the two, a hereditary trait is dened.

22- Dominant gene: gene that is in the genetic material and shows up physically 23- Recessive gene: gene that is in the genetic material, but doesnt show up physically. 24- Incomplete dominance: genes are not recessive or dominant, they combine. (Ex: a red ower and white ower that have pink offspring) 25- Evolution: concept developed by Darwin that states that organisms change slowly to adapt to their environment or as a result of random genetic combination. 26- Microevolution: the gene pool of a species changes but not the species itself. 27- Macroevolution: the entire species genes change to the point that it becomes a new species. 28- Genetic Drift: a gene that is lost through generations. 29- Sexual Selection: difference in physical appearances that make one member of a species more attractive than others. 30- Gene Flow: transfer of alleles from one population to another. 31- Speciation: appearance of a new species from an old one due to physical separation of the species into a new environment. P4- How Life Evolved: organic molecules were present on earth and eventually the got organized into proteins which formed the rst anaerobic prokaryotic organisms. Eventually, cyanobacteria that respire appeared and lled the atmosphere with oxygen allowing aerobic prokaryotes to appear. Finally, eukaryotic organisms appeared. 32- Autotroph: organism that makes its own food. 33- Heterotroph: organism that eats other organisms for food. 34- Monera Kingdom: Prokaryotic, unicellular and auto/heterotrophic. Ex: bacteria and cyanobacteria. 35- Protista Kingdom: Eukaryotic, uni/multicellular, and auto/heterotrophic. Ex: amoeba, algae, or mold. 36- Fungi Kingdom: Eukaryotic, uni/multicellular, and heterotrophic. Ex: yeast and mushrooms. 37- Plantae Kingdom: Eukaryotic, multicellular, and autotrophic. They have cell walls and carry out photosynthesis. They can be vascular (with capillaries that allow for high plants. Ex: trees) or non-vascular (without capillaries that limit height. Ex: moss).

38- Animalia Kingdom: Eukaryotic, multicellular, and heterotrophic. They can be vertebrate or invertebrate. 39- Hierarchy of Life: organizational scale which classies living systems according to size: organism < population < community < ecosystem < habitat < niche < biome < biosphere. 40- Organism: any individual living thing. 41- Population: any group of the same species living together. 42- Community: association of different populations that live in the same area. 43- Ecosystem: biological and non-biological parts of a community. 44- Habitat: place where organisms live. 45- Niche: the organisms role in the ecosystem. 46- Biome: large scale terrestrial communities shaped by its climate and classied by vegetation 47- Biosphere: all life and environments on earth. 48- Limiting factor: any factor that impedes a population from growing. it can be water, nutrients, or food sources. 49- Terrestrial ecosystems: forest and non-forest biomes. 50- Non-Terrestrial ecosystems: salt water and freshwater ecosystems. 51- Tropical Rainforest: warmth and rainfall year round. They have a lot of biodiversity and are very lush. almost all of its inhabitants live in the trees. 52- Temperate Forests: coniferous forests (forests that reproduce by cones and do not lose their leaves) or deciduous forests (forests that lose their leaves). They go through all four seasons. 53- Boreal forests: Mostly coniferous forests that experience a lot of cold year round. 54- Tropical Savanna: Trees are scarce and res keep their numbers low. They have wet and dry seasons. 55- Grasslands: Droughts that cannot sustain a forest and res that keep the grass from growing out of control.

56- Shrub land: Rainy winters and dry summers with res. They tend to appear near coasts. 57- Deserts: High evaporation that exceeds the amount of rainfall. Cacti grow here. 58- Tundra: very cold with no trees, but lots of grasses and mosses. There is a lot of permafrost and lots of migratory animals live here. 59- Mountain Zone: cannot support a frets because of the cold and elevation. 60- Lentic Ecosystem: standing water ecosystem. 61- Latic: running water ecosystems. 62- Wetlands: very active and biologically diverse. They take in rainwater and release it slowly and they purify water as well. 63- Photic zone: part of the sea which receives light. it is around 200 meters deep. 64- Detritus: dead organism that oat down to the bottom of the sea. 65- Chimiosynthesis: energy is produced from hydrogen sulde. 66- Sea: divided into an upper photic zone where most life is. The lower dark zone is sustained by the detritus that falls to the bottom, and the organisms that are chimiosynthetic. 67- Upwelling: ecosystems where currents carry nutrients from the sea oor. it is very rich in life. 68- Coral Reefs: they are on the shallow continental shelf and receive a lot of sunlight. There is a lot of symbiosis going on between them and algae. 69- Estuary: place where a river meets an ocean. they are nutrient rich thanks to rivers, and they contain a mix of slat and fresh water. Theyre either salt marshes, mud ats, or mangroves. 70- Mangroves: trees with very large and long intertwining roots that give shores structure and provide habitat. 71- Detrivores: they eat detritus. 72- Food Chain: movement of energy through trophic levels. 73- Trophic Level: group of organisms that are the same number of steps away from the primary producers. Only 10% of energy ows from one trophic level to another.

P5- How Mass and Energy Flow Through the Earth: mass is constant and almost never changes, while energy ow is linear. It comes from the sun, and then is radiated back into space. 74- Green House Gases: gases that trap heat in Earths atmosphere. P6- How Climate Change Works: it occurs when the amount of greenhouse gases increase allowing more heat to be trapped in Earths atmosphere. This changes weather patterns producing more extreme cycles, melting glaciers, changing migration patterns, and changing biological timing of natural processes. P7- C Cycle: At end of document. P8- N Cycle: At end of document. 75- Carbon Fixing: Autotrophs x C into a molecule. 76- Nitrogen Fixing: bacteria or lightning that transforms N2 to NO3. 77- N Fixing Bacteria: bacteria that transform N2 into biologically useful components like nitrates or ammonia. 78- Nitrifying Bacteria: they transform ammonia to nitrates. 79- Denitrifying Bacteria: they transform nitrates back into nitrogen. 80- Eutrophication: process by which a lake dies. P9- How Eutrophication Happens: when a lake has too much nitrogen in it, the algae grow without bounds. Because of their numbers, theyre not eaten fast enough and too much of them die and get decomposed by detrivores. They use oxygen for the decomposition and eventually reduce the lakes Oxygen content to the point that no life can be sustained. P10- P Cycle: At end of document. 81- Carrying Capacity: maximum number of population that can be sustained by the resources of a community. 82- Gauses Principle: at equilibrium, two species with identical source requirements cannot occupy the same habitat. 83- Monocrotophos: very toxic insecticide that is water soluble and biodegradable.

CS1- Grasshopper Population: When grasshoppers started to invade agricultural lands, monocrotophos was used to try and kill them off. What happened was that when they would die, eagles ,which were their natural predator, would eat them and get poisoned too. When the eagles started dying there were none left to keep the grasshoppers in check so the population exploded and things got even worse. 84- Deldrin: non-selective pesticide. CS2- Rats and Typhus: The above pesticide was used to try and kill mosquitoes that carried malaria. In doing so, not only were mosquitoes infected, but other bugs were too. Larger animals ate these bugs including cats. The cats started dying off in large numbers and then there was nothing to keep the rat population from expanding. This lead to an explosion of rats that carry diseases like typhus. 85- Human Population Growth Phases: they dene how industrially developed a nation is and they are four in number: - High birth rate and death rate - Declining birth and death rates. The death rate decreases faster. - Declining birth rate and leveling off of death rate. - Both rates level off The higher the phase, the more developed a nation is. 86- Ecological Footprint: the amount of land and water that each person needs to provide their basic needs. 87- Competition: type of relationship where species compete for resources 88- Predation: type of relationship where one species eats another. 89- Mutualism: type of relationship where both species help each other out. 90- Commensalism: type of relationship where one species benets from another and the other neither benets or is harmed. 91- Parasitism: type of relationship where one species benets from the other and the other gets harmed. 92- Symbiosis mutual or commensalist relationship in which one species lives within another. 93- Obligate: type of relationship where two species have to live together to survive. CS3- Lichen: it is the union of a fungus and an algae. The algae makes food for both of them through photosynthesis and the fungus provides shelter, support, and a water source. It is an obligate, symbiotic, mutualism.

CS4- Coral: it is the union of coral polyps and algae. The algae provides food for both of them and the coral provides carbon dioxide and shelter. It is an obligate mutual symbiosis. 94- Mycelium: type of fungus that grows from a spore. It grows in webs underground and has the typical umbrella fungus that spouts above ground. CS5- Mycorrhiza: union of mycelium and a plant. The fungus attracts water and nutrients for the plant while the plant makes sugars for both of them. It is a mutually symbiotic relationship. CS6- Gut Bacteria: They help organisms like humans or cows digest food properly while we provide them with a warm, sheltered environment. It is mutually symbiotic. CS7- Bees and Flowers: The bees get pollen to produce honey, and the owers get pollinated so they can reproduce. It is mutual but not symbiotic. CS8- Anemone and Clownsh: The anemone protects the sh, but stings any other sh that touches it. It is a symbiotic commensalism. 95- Diversity: measure of number of different species and species evenness in an ecosystem. 96- Simpson Dominance Index (D): probability that two individuals drawn at random from a community will belong to the same species. 97- Shannon Index (H): Indicates the evenness of species. The higher the index, the higher the diversity. 98- Diversity stresses: factors that make it harder for organisms to survive, but dont kill them. Temperature, Moisture, and amount of light are all stresses. 99- Disturbance: inuence on ecosystem that kills off a large amount of organisms. Events such as volcano eruptions or tsunamis fall into this category. 100- Intermediate Disturbance Hypothesis: it says that diversity is greatest at intermediate levels of stress, disturbance, and predation. Between the three they keep one species from dominating and maintain the possibility of more species living together. 101- C-Strategist: species that rely on outcompeting other species to dominate an ecosystem. 102- S-Strategist: species that rely on being stress tolerant to dominate an ecosystem. 103- R-Strategist: species that rely on fast reproduction to dominate an ecosystem.

104- CSR Theory: it says that a varying levels of stress and disturbances, different strategists thrive: -Low Stress/Disturbance: C-strategists thrive. -High Stress/ Low Disturbance: S-strategists thrive. -Low Stress/ High Disturbance: R-strategists thrive. -High Stress/Disturbance: Uninhabitable ecosystem. 105- Keystone Species: species that is small in number, but has a major inuence on its community. 106- Succession: ecosystem development following a disturbance or the creation of a new substrate. 107- Primary Succession: ecosystem starts barren from nothing. 108- Secondary succession: ecosystem starts from some level of life. It usually occurs due to a disturbance, like a re, and it is easier to progress from this succession. 109- Pioneer species: rst species to arrive into an ecosystem. They can live in highly inhospitable environments and they make it easier for other species to get established there. They are eventually replaced by other species. 110- Climax Stage: point during which an ecosystem has grown as large as it possibly can. K-strategists are high in numbers at climax, and before that R-strategists are high in number. CS10- Glacier Bay: it is in Alaska. The retreat of the glacier exposed barren land that started to develop through succession. Since it was all exposed slowly, the stages of succession can be seen clearly. The land that was exposed earlier is more developed, while the land that was exposed later is less developed. CS11- Red-cockaded woodpeckers: they live in savannas in south east US. The make nests in fungus infected tress because the wood is soft enough to peck through, but since it is still alive, it releases sap that wards off predators. They need a clear understory so predators wont climb on to trees and also so they can feed on insects. Cutting down these forests eliminates their home, but the US military preserves a large area of these tress for military training. The explosives they use cause articial res that keeps the ecosystem in balance. It all works out. 111- Infrastructure: fundamental facilities and systems serving a country, city, or area as transport, communication, system , power plant, and schools. The better it is, the higher the quality of life en economic systems. P11- How Electricity Gets to Our Homes: Power plants produce electricity at high voltages that go to a substation, and then a high voltage transmission line. These lines

span great distances and get the power to local substations which then pass it through transformers and transformer drums that both reduce voltage until it nally gets to our homes. 112- Eastern Interconnect: Huge electrical network that includes middle and eastern Canada and the East Half of the US. It is used for electricity trading. P12- How Natural Gas Gets To Us: It is rst pumped out if the ground and processed in a plant. The end product is pumped into a compression station. From here it is transported along extremely long pipes to anywhere that it is needed. Before being used, smell is added to the naturally odorless gas so leaks can be detected if they happen. T1 - Impacts of Infrastructure Roads Rely on Environment for: Impact on Environment: -Land -Aggregate -Asphalt -Habitat Fragmentation -Carbon dioxide emissions Nuclear -Uranium -Water -Radioactive Waste -Heat Nat. Gas -Ground Buildings -land -Concrete -Steel -Habitat loss -Heat -Water contamination

-Habitat loss -Green House Gasses

T2 - Water Infrastructure and Impacts Drinking Water Infrastructure -Water intake pipes -Water treatment plants -Water mains/pipes -Pumping stations -Storage tanks Sewer Water -Sewers -Pipes -Sewer treatments plants Storm Water -Catchment basins -Storm water pipes

Impacts

-Chemicals to treat -Sludge from water treatment - Fresh water to -Energy to pump treat - Electricity to pump

-Oil, salt, pesticides, metals from runoff -Erosion -Heat from asphalt.

113- Industrial Ecology: study of the interactions between ecosystems and industrial systems or between industrial systems.

114- Material Flow Analysis: systematic analysis of the ows of a material dened in space and time. 115- Life Cycle Assessment: it is a way of analyzing a product from the moment it is produced until it is disposed of. It is useful to compare different products at different stages. It is limited to the accuracy of data sources, changing markets, and environmental situations. It is very resource intensive and many assumptions must be made. 116- Sewage: water that buildings ush down after use. It contains nitrogen, phosphorous, human pathogens, metals, toxic organics, pharmaceuticals, endocrine disruptors, and biodegradable organics. 117- Biochemical Oxygen Demand (BOD): amount of oxygen in mg/L that is required to biodegrade organics. Ideally water should have between 10-15 mg/L, but life is sustainable until this number goes under 4 mg/L. 118- Raeration: when oxygen reenters water. 119- Dissolved Oxygen Sag Curve: combination of two curves. The rst curve is the oxygen demand curve which goes down, and the second one is the reaeration curve which goes up. The resulting curve has a sag and the lowest point tells you how low the BOD goes to see if it reaches unsafe levels. P13- How Sewage Is Treated: a- Screening to get out big objects, like trash b- Grit chamber where big particles settle c- Settling tank where smaller particles settle d- Water is treated microbially to remove organic compounds. It is passed through three chambers in the following order: anaerobic, anoxic, and aerobic e- Second settling tank to lter microbes f- Disinfection T3 - Sewage, treatment, and by-product In Sewage BOD Organic Matter N P Treated By d (aerobic) c, d (anaerobic) c, d (anaerobic/anoxic), e d (anaerobic), e By-Product Carbon Dioxide and Water Methane Nitrates and Solid N Biosolids

120- Constructed Wetlands: engineered wetlands that purify water

P13- How Constructed Wetland Purify Water: water comes in through a distribution pipe so it can be treated by the wetland. n The water can ow on the surface or under the soil. Through sedimentation the water gets treated by nitrifying and denitrifying bacteria. Plants reduce the P content along with salts that precipitate the P out of the water. The water then ows out of the wetland. 121- Cogeneration: producing electricity and steam for heat at the same time to save on heat production. 122- Combined Sewer: type of sewer which carries storm water and sewer water. It is prone to ooding when it rains or theres a lot of snow melting. 123- Green Roof: They are garden on roofs of buildings that reduce runoff, cool buildings, improve air quality, and provide habitat. The have the following layer from top to bottom: plants, growing medium, lter, drainage, root layer, and waterproof layer. T4 - Problems and Solutions Problems Transportation smog, GHG, resource use, habitat loss Heat lost in glass buildings, energy lost pumping water combined sewer overow, pollution (runoff takes waste to lakes/rivers), heat from asphalt goes to lakes/ rivers, erosion Solutions biking, public transport, carpooling, recycling car parts. less glass, solar thermal power, natural ventilation, rain water harvesting, cogeneration permeable pavements, rain water harvesting, rain garden, inltration, green roofs

Energy

Storm water

124- Habitat Fragmentation: breaking up of large habitats into smaller discontinuous habitats by roads, logging, or development. 125- Metapopulation: a collection of smaller, physically separated populations of the same species. If they drift far apart they can go extinct, but if they dont they can recolonize the area. 126- Satellite Populations: large core population of the species with small satellite populations that are colonized from the core to satellite.

CS12- Florida Panthers: Before European settlement they had high numbers, but hunting of deer, their natural food source, and the actual animal itself made the populations numbers go down drastically. Few panthers also meant low genetic variation and more defects. Eight female cougars were introduced and since then the population has gotten bigger. Establishing conservation areas, making it illegal to kill them, making highway over/underpasses for them, and reducing speed limits have all helped increase their numbers.