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$<em>2$, N$</em>2$.

• 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$<em>2$, N$</em>2$, CO$_2$; water vapor and trace gases.

• Gases are stable but react chemically to form new compounds.

• Plants take in CO$<em>2$ through leaves; animals take in O$</em>2$ 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$<em>4$·2H$</em>2$O.

• Gypsum has a predictable pattern of atoms held closely together → CaSO$<em>4$·2H$</em>2$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$<em>2$, H$</em>2$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$<em>2$, H$</em>2$O, N, P, K, Ca, Fe.

1) Carbon Cycle

• Begins with atmospheric CO$<em>2$; CO$</em>2$ 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$<em>2$ in the atmosphere; photosynthesis removes about 175 Gt/year; deforestation and soil degradation release significant amounts of CO$</em>2$; 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$<em>4^+$) and nitrate (NO$</em>3^-$).

• 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$<em>2$ to NH$</em>4^+$ 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$<em>3^-$ is reduced to N$</em>2$ (released to atmosphere) via intermediate forms such as NH$<em>4^+$, NO$</em>2^-$, NO, N$<em>2O, N$2$.</p></li><li><p>Nitrogen cycle diagram shows relationships among N$2$ in air, soil bacteria, NO$3^-$, NH$4^+$, NO$2^-$, NO, N$2$O, N$2$.</p></li></ul><h3 id="3417fe42-7e17-4ff7-98bc-985f5684320a" data-toc-id="3417fe42-7e17-4ff7-98bc-985f5684320a" collapsed="false" seolevelmigrated="true">4) Sulfur Cycle</h3><ul><li><p>Sulfur is a component of proteins, hormones, vitamins; often linked with oxygen as sulfate (SO$_4^{2-}$).</p></li><li><p>Most sulfur is in rocks, minerals, and ocean sediments.</p></li><li><p>Pathways into the atmosphere/soil include weathering, volcanic activity, fossil fuel combustion (coal, petroleum), and mining of metals.</p></li><li><p>Plants and microbes uptake sulfate from soil.</p></li><li><p>Environmental impacts:</p><ul><li><p>Sulfur aerosols can temporarily cool the atmosphere.</p></li><li><p>Acid rain produced environmental problems; polluted water bodies in the Northeast in the 1950s–70s.</p></li><li><p>Sulfur dioxide (SO$x$) emissions are restricted for power plants; reductions include about 40$x$ 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: $6\,CO<em>2 + 6\,H</em>2O + \text{light energy} \rightarrow C<em>6H</em>{12}O<em>6 + 6\,O</em>2$

• Cellular respiration: $C<em>6H</em>{12}O<em>6 + 6\,O</em>2 \rightarrow 6\,CO<em>2 + 6\,H</em>2O + \text{energy}$

• Gypsum formula: CaSO$<em>4$·2H$</em>2$O

• Calcium, oxygen, sulfur, hydrogen interplay in minerals is exemplified by gypsum (CaSO$<em>4$·2H$</em>2$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.