Study Notes: Chapter 3 – Organisms in Their Environment
Matter and Energy in the Environment
Chapter and course context: Organisms in their environment; focus on matter, energy, and how ecosystems function through interactions among Earth’s spheres and cycles.
Atoms, Elements, Molecules, and Compounds
Matter: anything that occupies space and has mass; includes all solids, liquids, gases, living and nonliving things.
Atoms: building blocks of all matter; smallest representative sample of an element; composed of protons, neutrons, and electrons.
Elements: substances that cannot be separated into simpler substances by chemical means; there are 94 naturally occurring elements.
Molecule: two or more atoms bonded in a specific way; properties depend on how atoms are bonded (e.g., O$2$, N$2$).
Compound: substance of two or more different elements/atoms chemically united in definite proportions (e.g., methane, CH$_4$).
Molecules and compounds can be assembled and disassembled repeatedly in chemical processes.
Chemical Bonding, Reactions, and Conservation of Matter
Chemical reactions rearrange atoms to form different kinds of matter.
Law of Conservation of Matter: atoms do not change; they are not created or destroyed during chemical reactions; they are rearranged.
The Four Spheres of the Earth
4 spheres: Atmosphere, Hydrosphere, Lithosphere, Biosphere (living systems).
Biosphere is the sum of interconnected and interdependent spheres in global processes; living organisms use materials from the other three spheres to build molecules (chemical compounds).
Each sphere contains components essential to life and interacts with the others through transport of matter and energy.
1) Atmosphere
Thin layer of gases separating Earth from outer space.
Major components: Oxygen (O$2$), Nitrogen (N$2$), Carbon Dioxide (CO$_2$); water vapor and trace gases are also present.
Gases are normally stable but can react chemically to form new compounds.
Plants respire CO$2$ through leaves; animals take in O$2$ via lungs, gills, or skin.
2) Hydrosphere
All water: oceans, rivers, ice, groundwater; source of hydrogen.
Water exists as solid (ice, snow) below freezing, as liquid above freezing and below vaporization, and as vapor above vaporization.
3 states of water (transitions)
Solid (ice) → Melting → Liquid (water) [energy input]
Liquid → Freezing → Solid (ice) [energy release]
Liquid → Evaporation → Gas (water vapor) [energy input]
Gas → Condensation → Liquid [energy release]
Solid → Sublimation → Gas [energy input]
Gas → Deposition → Solid [energy release]
3) Lithosphere
Rigid outer part of Earth consisting of crust and upper mantle.
Mineral: naturally occurring solid with a hard, crystalline structure and a defined chemical composition; atoms bonded by attractions between charged particles.
All elements essential for life occur in mineral form (e.g., zinc, sodium, chloride).
Rocks: composed of small crystals of two or more minerals.
Soil: particles of many different minerals.
Example: Gypsum with a predictable pattern of atoms, CaSO$4$·2H$2$O.
Calcium, Oxygen, Sulfur, Hydrogen are common elements in minerals like gypsum.
Gypsum example
Gypsum has the formula CaSO$4$·2H$2$O, illustrating how minerals can include water of crystallization (hydration).
4) Biosphere
Sum of all interconnected and interdependent spheres in global processes; the living systems.
Interconnections: organisms use materials from Atmosphere, Hydrosphere, and Lithosphere to build organic molecules.
Interactions Between Spheres
Air, water, and minerals interact; water is a solution containing dissolved gases and minerals (solutes).
Water cycles between spheres via evaporation, condensation, precipitation; atmospheric moisture fluctuates.
Wind can transport dust and mineral particles over large distances.
Dissolved minerals and gases travel between the three spheres within the biosphere.
Chemical compounds, minerals, gases, and water cycle through Atmosphere, Hydrosphere, and Lithosphere.
Organic vs. Inorganic Compounds and Essential Elements
Organic compounds: large molecules made by living organisms; contain carbon-hydrogen (C–H) bonds.
Major organic biomolecules: proteins, carbohydrates, lipids, nucleic acids (DNA, RNA).
Six key elements in organic compounds: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Phosphorus (P), Sulfur (S).
Inorganic compounds: lack carbon–carbon or carbon–hydrogen bonds (e.g., CO$2$, H$2$O, N$_2$).
Essential elements: those necessary for life (e.g., C, H, O); many simple inorganic compounds circulate in hydrosphere, lithosphere, and atmosphere; complex organic compounds dominate in the biosphere.
Energy: Form, Measurement, and Thermodynamics
The universe is made of matter and energy.
Energy (E): the ability to move matter; heat energy measures the movement of atoms and molecules.
Common forms: light, heat, motion, electricity; energy has no mass and does not occupy space.
Energy changes the position or state of matter (e.g., explosions move matter; heating water causes phase change).
Types of Energy
Kinetic energy (E$_k$): energy in action or motion (e.g., light, heat, physical motion, electrical current).
Potential energy (E$_p$): energy stored for later use (e.g., propane, stretched rubber bands).
Chemical energy: potential energy stored in chemical bonds; bonds break in chemical reactions to release energy.
Measuring Energy
Energy can be transformed from one form to another (potential to kinetic, etc.).
Energy is commonly measured in calories (calories measure heat required to raise the temperature of 1 gram of water by 1°C).
Temperature measures molecular motion; changes in temperature reflect changes in kinetic energy.
Movement of matter requires energy input or release; changes in energy drive changes in matter.
Laws of Thermodynamics
First Law (Law of Conservation of Energy): Energy is neither created nor destroyed; it can be converted from one form to another.
Second Law: Usable energy decreases in any energy conversion; total entropy of a system cannot decrease over time.
Entropy: a measure of disorder; increasing entropy means increasing disorder; without energy input, systems trend toward greater entropy and heat release.
Energy Storage and Flow in Ecosystems
Energy storage and release example: energy can be input (e.g., light) and stored as high-potential-energy biomass, then released through cellular processes.
Photosynthesis stores energy in biomass; cellular respiration releases energy from biomass.
Producers and Primary Energy Capture: Photosynthesis
Producers convert low-potential-energy raw materials into high-potential-energy organic compounds (sugars).
Production of organic molecules from inorganic material represents a gain in potential energy; breakdown releases energy.
Photosynthesis (in plants)
Chlorophyll absorbs kinetic light energy to drive production of organic compounds.
Plants photosynthesize: carbon dioxide + water + light energy → sugar (glucose) + oxygen.
Chemical equation:
6\ \mathrm{CO2} + 6\ \mathrm{H2O} + \text{light energy} \rightarrow \mathrm{C6H{12}O6} + 6\ \mathrm{O2}
Glucose (C$6$H${12}$O$_6$) serves as the backbone for other organic compounds and provides energy for cellular activities (growth, reproduction).
Glucose can be stored as starch in grains or as oil in seeds.
Enzymes: proteins that catalyze biochemical reactions during photosynthesis (synthesis and breakdown of chemical bonds).
Cellular Respiration and Energy Use
Consumers rely on energy stored in organic matter produced by producers.
Cellular respiration: sugars are broken down inside cells to release usable energy; oxygen is consumed; CO$2$ and H$2$O are produced as by-products.
Equation:
\mathrm{C6H{12}O6} + 6\ \mathrm{O2} \rightarrow 6\ \mathrm{CO2} + 6\ \mathrm{H2O} + \text{energy}
In the plant, glucose produced by photosynthesis is used for growth, maintenance, and reproduction; can be stored as starch or oil.
Efficiency: cellular respiration is typically only 40–60% efficient; the remainder of energy is released as heat or stored in other forms.
Anaerobic respiration (fermentation) yields less energy than oxidation and occurs in oxygen-poor environments.
Energy Flow Versus Nutrient Cycles
Energy flow through ecosystems is largely one-way: solar energy is captured and eventually dissipated as heat; nutrients are recycled.
Most solar energy entering ecosystems is captured by plants (2–5%); the rest heats air, water, and land and is eventually radiated back to space.
Nutrients (elements) cycle repeatedly through biogeochemical cycles; energy flow is not recycled in the same way.
Four Key Nutrient Cycles
Nutrients are elements essential for growth, maintenance, repair, and cellular energy in organisms (plants and animals).
The four important cycles are: Carbon, Phosphorus, Nitrogen, and Sulfur.
1) Carbon Cycle
Begins with atmospheric CO$_2$ as a reservoir.
Carbon is metabolized into organic molecules in organisms; it is respired back to air or deposited as soil detritus.
Ocean photosynthesis: CO$_2$ dissolves in seawater and is incorporated into marine organisms via phytoplankton and green algae, moving carbon through marine food webs.
Respiration returns inorganic carbon (CO$2$) to seawater; combustion of fossil fuels releases CO$2$ into the atmosphere.
Limestone (CaCO$_3$) sequesters carbon; weathering releases carbon back into circulation.
Global carbon cycle highlights:
875\ ext{Gt CO}_2 in the atmosphere.
Photosynthesis removes roughly 175\ ext{Gt/year} of CO$_2$.
Deforestation and soil degradation release significant CO$_2$ to the atmosphere; reforestation enhances sequestration.
Global carbon cycle diagram relationships: Atmosphere ⇆ Ocean ⇆ Soils ⇆ Plants/Animals ⇆ Decomposers.
Additional notes:
The cycle includes processes such as combustion of fossil fuels, limestone weathering, and detrital deposition.
Ocean-atmosphere exchange is a major interface for carbon transfer.
2) Phosphorus Cycle
Phosphorus originates in rocks and soils as inorganic phosphate (PO$_4^{3-}$).
Weathering releases phosphate; plant uptake incorporates PO$_4^{3-}$ into organic compounds.
Phosphorus is essential but often a limiting nutrient in ecosystems; shortages constrain productivity.
Phosphorus is mined and used in fertilizers, animal feeds, and detergents; large anthropogenic inputs stimulate production but can cause pollution.
Excess phosphorus in water bodies causes eutrophication: algal blooms, bacteria overgrowth, fish kills, and the formation of dead zones (e.g., northern Gulf).
Global phosphorus cycle notes:
Not connected to the atmosphere.
Fertilizer runoff and leaching from agriculture and lawns contribute to environmental loading.
Diagrammatic flow: rock/soil → weathering → PO$_4^{3-}$ in soil → plant uptake → organic phosphate in biomass → decomposition → return to soil; human inputs via mining and fertilizers amplify flows.
3) Nitrogen Cycle
Atmosphere is the main reservoir of nitrogen (N$2$) at 78% by volume; most organisms cannot use N$2$ directly.
Reactive nitrogen (Nr) forms usable forms like ammonium (NH$4^+$) and nitrate (NO$3^-$).
Soil, water, and sediments host bacteria that convert nitrogen to usable forms (nitrogen fixation, nitrification, etc.).
Key processes:
Nitrogen fixation: converts N$2$ to Nr (e.g., NH$4^+$ or NO$_3^-$).
Nitrification: soil bacteria convert ammonium to nitrate for plant uptake.
Denitrification: in low-oxygen soils, microbes reduce nitrate to N$_2$ gas, returning nitrogen to the atmosphere.
Plant uptake: Nr ions are incorporated into proteins and nucleic acids; nitrogen moves through the food web and returns to the environment via wastes and decomposition.
Nitrogen fixation sources:
Biological: nitrogen-fixing microbes in legume root nodules (e.g., peas, beans, soybeans, alfalfa) provide usable N in exchange for energy.
Atmospheric fixation: lightning.
Industrial fixation: Haber-Bosch process (1909) for fertilizer production.
Combustion of fossil fuels releases oxidized nitrogen species (NOx).
Non-legume crops often receive nitrogen fertilizer; agricultural practices have increased the rate of nitrogen transfer from air to land, with pollution implications for air and water.
4) Sulfur Cycle
Sulfur is a component of proteins, hormones, and vitamins; commonly appears as sulfate (SO$_4^{2-}$).
Most sulfur is stored in rocks, minerals, and ocean sediments.
Pathways into air or soil include weathering, volcanic activity, fossil fuel combustion (coal, petroleum), and mining of metals.
Plants and microbes uptake soil sulfate; sulfur cycles through ecosystems.
Environmental impacts:
Sulfur aerosols can temporarily cool the atmosphere when deposited on land.
Acid rain arises from sulfur dioxide (SO$_x$) emissions; restricted emissions have reduced acid rain in several regions.
Global sulfur cycle involves interactions among plants, soils, oceans, atmosphere, volcanoes, factories, and wetlands.
Nutrient Cycles and Energy Flow: Integrated View
Nutrient cycles ensure continuous availability of inorganic nutrients (e.g., CO$2$, H$2$O, N, P, K, Ca, Fe) to ecosystems.
Detritus and decomposers play essential roles in recycling nutrients:
Detritus: organic matter from dead organisms and waste.
Detritivores and decomposers (fungi and bacteria) break down detritus, releasing inorganic nutrients back into the environment.
Energy flow pathways:
Energy enters as sunlight, flows through producers, primary and higher-level consumers, detritus feeders, and decomposers, and is ultimately dissipated as heat.
Unlike nutrients, energy is not recycled in a closed loop; it flows in one direction and must be replenished by ongoing solar input.
Real-World Relevance and Implications
Human activities (deforestation, fossil fuel combustion, mining, agriculture) significantly alter carbon, nitrogen, phosphorus, and sulfur cycles.
Climate implications: atmospheric CO$_2$ levels influence climate; carbon sequestration via forests and soils matters for mitigating climate change.
Eutrophication risks from excessive phosphorus and nitrogen inputs lead to dead zones and biodiversity loss in aquatic systems.
Acid rain historically affected freshwater and soil chemistry; reductions in SO$_2$ emissions show measurable environmental benefits.
Ethical and practical considerations:
Balancing food production (phosphorus and nitrogen inputs) with ecological integrity and water quality.
Managing energy resources to minimize disruptive environmental feedbacks and promote sustainable ecosystems.
Key Formulas and Notable Numbers (LaTeX)
Photosynthesis: 6\ \mathrm{CO2} + 6\ \mathrm{H2O} + \text{light energy} \rightarrow \mathrm{C6H{12}O6} + 6\ \mathrm{O2}
Cellular respiration: \mathrm{C6H{12}O6} + 6\ \mathrm{O2} \rightarrow 6\ \mathrm{CO2} + 6\ \mathrm{H2O} + \text{energy}
Atmospheric carbon dioxide reservoir: 875\ \text{Gt CO}_2
Carbon removal by photosynthesis: 175\ \text{Gt/year}
Energy flow efficiency to plants: 2\% \text{ to } 5\% of solar input captured by plants
Energy forms classification:
Kinetic energy: E_k
Potential energy: E_p
Chemical energy: E_{chem}
Entropy concept: S \uparrow \text{ (increasing disorder) as energy is dispersed}
Fossil fuel impact on carbon cycle intro: combustion releases CO$_2$ into the atmosphere
Connections to Foundational Principles
Matter conservation underpins chemical changes in biological systems (atoms rearranged but not created/destroyed).
Energy flow governs ecological processes; the sun as the primary energy source drives photosynthesis, which fuels entire ecosystems.
Biogeochemical cycles connect biology with geology and chemistry; nutrient availability shapes ecosystem productivity and health.
Summary Takeaways
The Earth's biosphere depends on the interaction of Atmosphere, Hydrosphere, Lithosphere, and living organisms.
Organic compounds with C–H bonds form the basis for life; energy is stored in chemical bonds and released through metabolism.
Photosynthesis stores solar energy in biomass, while respiration releases it for cellular work; only a portion is captured efficiently.
Nutrient cycles (C, P, N, S) move elements through ecosystems, while energy flows in a one-way path from the sun to heat sink.
Human actions alter these cycles, with significant ecological and ethical implications for sustainability and environmental health.