Organisms in Their Environment - Comprehensive Notes
Units of Matter
Matter: anything that occupies space and has mass; includes all solids, liquids, and 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; 94 naturally occurring atoms.
Atoms and Elements
Molecule: two or more atoms bonded in a specific way; properties depend on how atoms are bonded; examples include oxygen gas and nitrogen gas → O$2$, N$2$.
Compound: a substance of two or more different elements/atoms chemically united in definite proportions; example: methane gas → CH$_4$.
Molecules and compounds are used, assembled, and disassembled repeatedly.
Atomic Structure (illustrative)
Atoms contain electrons and protons (and neutrons in the nucleus).
Examples shown include hydrogen and carbon configurations.
Law of Conservation of Matter
Chemical reactions rearrange atoms to form different kinds of matter.
Law: atoms do not change; they are not created or destroyed.
Four Spheres of the Earth
Atmosphere (air)
Hydrosphere (water)
Lithosphere (rock/soil)
Biosphere (living systems)
The biosphere is the sum of interconnected living systems and uses materials from the other three spheres to build molecules.
Atmosphere
Thin layer of gases separating Earth from outer space.
Major components: O$2$, N$2$, CO$_2$; water vapor and trace gases.
Gases are stable but react chemically to form new compounds.
Plants take in CO$2$ through leaves; animals take in O$2$ through lungs, gills, or skin.
Hydrosphere
All water in oceans, rivers, ice, groundwater; source of hydrogen.
Water can exist as solid (ice, snow) below freezing, or liquid above freezing but below vaporization.
States of Water
Solid (ice) → Melting → Liquid (water)
Liquid → Vaporization (evaporation) → Gas (vapor)
Gas → Condensation → Liquid
Gas → Solid (deposition)
Solid → Gas (sublimation)
Energy changes accompany phase changes; energy required or released during transitions.
Lithosphere
Rigid outer part of Earth consisting of crust and upper mantle.
Mineral: naturally occurring solid formed by geologic processes; hard, crystalline structure; atoms bonded by attraction between positive and negative charges.
All elements required by organisms for life are present in mineral form (e.g., Zn, Na, Cl).
Rocks: composed of small crystals of two or more minerals.
Soil: particles of many different minerals.
Gypsum Example
Elements: Calcium, Oxygen, Sulfur, Hydrogen.
Gypsum: CaSO$4$·2H$2$O.
Gypsum has a predictable pattern of atoms held closely together → CaSO$4$·2H$2$O.
Biosphere
Sum of interconnected and interdependent spheres in global processes; the living systems.
A, Atmosphere; B, Hydrosphere; C, Lithosphere.
Living organisms in the biosphere use materials from the other three spheres to build molecules (chemical compounds).
Interactions Between Spheres
Air, water, and minerals interact with each other.
Water is a solution containing dissolved gases and minerals (solutes).
Water enters the atmosphere through evaporation; leaves via condensation or precipitation.
Air moisture fluctuates; wind carries dust or mineral particles.
Dissolved minerals and gases travel between spheres; mineral dissolution and crystallization; precipitation; gas exchange.
Organic Compounds
Organisms are composed of large compounds: proteins, carbohydrates (sugars, starches), lipids (fats), nucleic acids (DNA, RNA).
Six key elements: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Phosphorus (P), Sulfur (S).
Organic vs. Inorganic Compounds
Organic: compounds with carbon–carbon or carbon–hydrogen bonds; e.g., most compounds in living things.
Inorganic: compounds with no carbon–carbon or carbon–hydrogen bonds; e.g., CO$2$, H$2$O, N$_2$.
Essential elements for life include C, H, O; simple inorganic compounds in hydrosphere, lithosphere, and atmosphere; complex organic compounds in the biosphere.
Natural organic compounds are made by living organisms; synthetic organic compounds are human-made (e.g., Testosterone YK-11).
Energy and Thermodynamics
The universe is made up of matter and energy; energy is the ability to move matter.
Energy forms include light, heat, movement, electricity; energy has no mass and does not occupy space.
Energy can change position or state of matter; energy changes drive matter movement.
First Law of Thermodynamics (Law of Conservation of Energy): energy is neither created nor destroyed; it can be converted from one form to another.
Second Law of Thermodynamics: usable energy is lost in any energy conversion; total entropy of a system cannot decrease with time.
Entropy: a measure of disorder in a system; increasing entropy means increasing disorder; without energy input, systems move toward higher entropy and release heat.
Types of Energy
Kinetic energy: energy in action or motion (e.g., light, heat, physical motion, electrical current).
Potential energy: energy stored in position or state (e.g., propane, stretched rubber bands).
Chemical energy: potential energy stored in chemical bonds; released when bonds break in chemical reactions.
Measuring Energy
Energy can be transformed between forms (potential ↔ kinetic; e.g., charging a battery).
Energy is often measured in calories.
Calorie: amount of heat required to raise the temperature of 1 gram of water by 1 degree Celsius.
Temperature measures molecular motion; movement of matter requires energy absorption or release; changes in matter require changes in energy.
Energy Flow in Ecosystems
Most solar energy entering ecosystems is absorbed and heats the atmosphere, oceans, and land.
Only about 2–5% is captured by plants.
All energy eventually escapes as heat (re-radiated to space); entropy increases.
Energy flows in a one-way direction through ecosystems (OUT); nutrients are recycled via biogeochemical cycles.
Nutrient Cycles and Energy Flow (Overview)
Nutrients: elements necessary for growth, maintenance, repair, and cellular energy in organisms; required by plants and animals.
Producers convert inorganic nutrients to organic molecules; detritus and decomposers recycle nutrients.
The four important cycles: Carbon, Phosphorus, Nitrogen, Sulfur.
Inorganic nutrients from environmental sources include CO$2$, H$2$O, N, P, K, Ca, Fe.
1) Carbon Cycle
Begins with atmospheric CO$2$; CO$2$ is metabolized into organic molecules in organisms.
Carbon is respired by plants and animals back into the air or deposited as detritus in soil.
In oceans, photosynthesis dissolves CO$_2$ in seawater via phytoplankton and green algae; carbon moves through marine food webs.
Respiration returns inorganic carbon (CO$_2$) to seawater.
Exchanges occur between atmosphere and water interfaces.
Fossil fuels combustion releases CO$_2$.
Fossilization of dead plants/animals forms coal, petroleum, diamonds; limestone (CaCO$_3$) sequesters carbon; weathering releases carbon.
Global carbon cycle diagram shows fluxes between pools: Atmosphere, Ocean, Soils, Plants/Detritus, Fossil fuels, Limestone, Decomposers, etc.
Quantitative notes: 875 Gt of CO$2$ in the atmosphere; photosynthesis removes about 175 Gt/year; deforestation and soil degradation release significant amounts of CO$2$; reforestation improves CO$_2$ sequestration.
2) Phosphorus Cycle
Phosphorus originates in rocks/soil as inorganic phosphate PO$_4^{3-}$.
Weathering releases phosphate; phosphorus often a limiting nutrient in some ecosystems due to shortages.
Plants incorporate PO$_4^{3-}$ into organic compounds (organic phosphate) from soil/water; decompose to release phosphate back into environment.
Phosphorus is mined for fertilizers, animal feeds, detergents; large global inputs from agricultural fertilizer.
Excess phosphorus in water causes eutrophication: algal and bacterial overgrowth, fish die-offs, and formation of a dead zone (e.g., northern Gulf).
Not connected to the atmosphere.
3) Nitrogen Cycle
Air is the main reservoir of nitrogen (N$_2$) comprising about 78% of the atmosphere.
Nitrogen is essential for plants; most organisms cannot use N$_2$.
Reactive nitrogen (Nr) forms usable by organisms include ammonium (NH$4^+$) and nitrate (NO$3^-$).
Bacteria in soil, water, and sediments convert nitrogen to usable forms.
Nitrogen fixation processes:
Biological fixation: nitrogen-fixing microbes in legume root nodules convert N$2$ to NH$4^+$ or NO$_3^-$; legumes provide habitat/food for bacteria and obtain usable nitrogen.
Atmospheric fixation: lightning fixes nitrogen.
Industrial/chemical fixation: Haber–Bosch process (1909) converts nitrogen to usable forms for fertilizers.
Combustion of fossil fuels: NO$_x$ species form reactive nitrogen.
Plants take up Nr and incorporate into proteins and nucleic acids; nitrogen moves through the food web to decomposers.
Agricultural practices have more than doubled the rate of nitrogen moving from air to land, increasing atmospheric and aquatic pollution.
Legumes (peas, beans, soybeans, alfalfa) fix nitrogen; non-leguminous crops (corn, wheat, potatoes) receive nitrogen via industrial fixation.
Denitrification: in oxygen-poor soils/sediments, microbes use nitrate for anaerobic respiration; NO$3^-$ is reduced to N$2$ (released to atmosphere) via intermediate forms such as NH$4^+$, NO$2^-$, NO, N$2O, N$2$.
Nitrogen cycle diagram shows relationships among N$2$ in air, soil bacteria, NO$3^-$, NH$4^+$, NO$2^-$, NO, N$2$O, N$2$.
4) Sulfur Cycle
Sulfur is a component of proteins, hormones, vitamins; often linked with oxygen as sulfate (SO$_4^{2-}$).
Most sulfur is in rocks, minerals, and ocean sediments.
Pathways into the atmosphere/soil include weathering, volcanic activity, fossil fuel combustion (coal, petroleum), and mining of metals.
Plants and microbes uptake sulfate from soil.
Environmental impacts:
Sulfur aerosols can temporarily cool the atmosphere.
Acid rain produced environmental problems; polluted water bodies in the Northeast in the 1950s–70s.
Sulfur dioxide (SO$x$) emissions are restricted for power plants; reductions include about 40% in SO$x$ emissions and a roughly 65% drop in acid rain levels.
Global Cycles and Energy Context
Global cycles are not isolated; energy from the sun drives nutrient cycles and energy flow in ecosystems.
Detritus (dead organic matter) and decomposers are central to nutrient recycling.
The role of producers (plants) is to capture solar energy and convert inorganic nutrients into organic energy-rich compounds.
Key Examples and Formulas (LaTeX)
Photosynthesis:
Cellular respiration:
Gypsum formula: CaSO$4$·2H$2$O
Calcium, oxygen, sulfur, hydrogen interplay in minerals is exemplified by gypsum (CaSO$4$·2H$2$O).
Quick Summary of Quantitative Highlights
CO$_2$ in the atmosphere: ~875 Gt
CO$_2$ removal by photosynthesis: ~175 Gt/year
Energy capture by plants from sunlight: ~2–5% of solar input
Cellular respiration efficiency: about 40–60%
Sulfur-related reductions: SO$_x$ emissions reduced by ~40%; acid rain levels reduced by ~65%
Key chemical cycles do not rely on a single source but integrate atmosphere, hydrosphere, lithosphere, and biosphere to sustain life on Earth.