Chapter 2 Notes: Matter, Energy, and Geology

Central Case Study: The Tohoku Earthquake

In 2011, Japan experienced a massive 9.0 magnitude earthquake along the coast, which generated a tsunami. The resulting surge overtopped a 5.7-meter seawall protecting the Fukushima Daiichi nuclear power plant, flooding its emergency generators. This case highlights how energy, matter, and chemistry interact with real-world infrastructure and safety concerns, illustrating why understanding physical systems matters in predicting and mitigating environmental hazards.

Matter, Chemistry, and the Environment

Matter is defined as any material that has mass and occupies space, while chemistry studies the interaction of matter. To understand events like Fukushima, one must grasp the basic properties of matter and energy and how they transform and interact within environmental systems. The environment is a stage where matter and energy constantly cycle, transforming substances but never being created or destroyed in the sense of the global balance described by conservation principles. The Fukushima accident underscores how pollutants and radioactive materials persist in ecosystems; undesirable matter cannot be simply destroyed and requires management, containment, or transformation rather than annihilation.

Matter is Conserved

The law of conservation of matter states that matter can be transformed from one type of substance to another, but it cannot be created or destroyed. In ecosystems, matter cycles continuously through processes such as photosynthesis, decomposition, and mineralization. When contaminants like nuclear waste enter the environment, they persist and cycle through air, water, and biota rather than vanishing, highlighting the need for long‑term monitoring and remediation strategies.

Atoms and Elements: Chemical Building Blocks

Nuclear reactors rely on uranium, an element used to power certain reactor designs. Elements are substances with specific properties that cannot be broken down into substances with different properties. They are organized and studied according to the periodic table. The most abundant elements in the Earth include oxygen, hydrogen, silicon, nitrogen, and carbon, which lay the foundation for the chemistry of rocks, water, and living organisms.

Atomic Structure: Protons, Neutrons, and Electrons

Atoms are the smallest units that retain an element’s chemical properties. Each atom comprises three main types of subatomic particles: protons (positively charged) that determine the atomic number, neutrons (neutral), and electrons (negatively charged) that orbit the nucleus. Protons and neutrons reside in the dense nucleus, which gives the atom its mass. Electrons orbit around the nucleus and are held in orbit by electrostatic attraction to the positively charged protons. The mass number of an atom is the sum of its protons and neutrons.

Isotopes, Ions, and Atomic Variability

Within an element, the number of protons remains constant, but the number of electrons can vary, producing ions with positive or negative charges. Neutron number can also vary, giving isotopes with different masses. Isotopes have special notations indicating their atomic mass. Some isotopes are radioactive, meaning they decay by emitting subatomic particles and high-energy radiation, thereby changing their identity over time. These radioisotopes are most harmful when taken into living organisms through ingestion or inhalation. After Fukushima, scientists began regularly testing foods and drinking water for radioisotopes to monitor potential exposure.

Radioisotopes decay into smaller and smaller radioisotopes until they reach a stable form. The half-life of an isotope is the time required for half of its atoms to decay. Cesium, a radioisotope detected in the ocean after nuclear accidents and weapons testing, has a half-life of about t_{1/2} \,=\, 30\,\text{years}. As radioisotopes decay, their activity diminishes, but the original contamination can persist for many years depending on the half-lives involved.

Atoms may also gain or lose electrons, becoming charged ions. The charge of an ion indicates the net loss or gain of electrons. For example, \mathrm{Ca^{2+}} has lost two electrons. Radiation energy emitted by radioisotopes is called ionizing radiation because it can ionize molecules, altering their stability and potentially damaging biological tissues.

Bonding: Molecules, Compounds, and Mixtures

Atoms bond to form molecules, and molecules combine to form compounds. A molecule is a stable combination of two or more atoms bonded together, such as \mathrm{O2}. If the molecule contains two or more different elements, it is a compound, such as water \mathrm{H2O} or carbon dioxide \mathrm{CO_2}. Bonds arise from the attraction between atoms’ electrons.

Covalent bonds form when electrons are shared between atoms. In water, unequal sharing creates pole-like regions with partial charges, enabling hydrogen bonding—an essential but relatively weak interaction between water molecules that stabilizes many biological structures. When the attraction within a molecule is sufficiently unequal, an electron can be transferred from one atom to another, producing oppositely charged ions that attract each other to form an ionic bond. Atoms and molecules can also form mixtures, where substances do not react with one another. Evenly distributed mixtures are called solutions.

Water’s Chemistry Facilitates Life

Water has several unique properties that support life: it is the universal solvent, capable of dissolving many charged molecules; it can absorb a large amount of heat without large temperature changes, acting as an effective heat buffer; and ice is less dense than liquid water, causing ice to float and insulate underlying waters from freezing solid. These properties underpin climate regulation and the stability of aquatic ecosystems.

Acidity, Bases, and the pH Scale

In aqueous solutions, water self‑ionizes into hydrogen ions (H+) and hydroxide ions (OH−). Pure water contains equal concentrations of both and is neutral. Acids have higher hydrogen ion concentrations, while bases (alkaline solutions) have higher hydroxide ion concentrations. The pH scale quantifies acidity or basicity: pure water has [H^+] = 10^{-7} M and a pH of 7. Acids have pH values below 7, and bases have pH values above 7. The pH scale is logarithmic, meaning each whole number change represents a tenfold change in hydrogen ion concentration: for example, a solution with a pH of 6 has ten times the hydrogen ion concentration of a solution with pH 7.

Organic and Inorganic Compounds

Matter is classified as organic or inorganic. Organic compounds contain carbon atoms joined by covalent bonds. A key group of organic compounds is the hydrocarbons, which consist solely of hydrogen and carbon. Fossil fuels and many plastics are predominantly hydrocarbons. Inorganic compounds, by contrast, do not primarily consist of carbon–hydrogen bonds.

Macromolecules: The Building Blocks of Life

Organic compounds also include polymers, long chains formed by repeating units. Polymers and lipids are large macromolecules. Proteins are polymers composed of amino acids and perform countless roles in organisms—from building tissues to catalyzing chemical reactions as enzymes. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), carry hereditary information and blueprint the production of proteins. Nucleic acids are polymers made of nucleotides, and specific regions of DNA that encode particular proteins are genes. Carbohydrates include simple sugars like glucose and complex carbohydrates like cellulose and chitin, which are found in plant cell walls and insect exoskeletons, respectively. Lipids form a diverse group of molecules that do not dissolve in water: fats and oils store energy, waxes provide structural roles, and steroids form part of hormonal signaling.

Energy: The Capacity to Change Matter

Energy is the capacity to change the position, composition, or temperature of matter. When energy causes movement, it performs work. Energy exists in multiple forms and can be transformed from one form to another, but total energy remains conserved.

Energy Forms: Potential and Kinetic

Potential energy is the energy of position or composition, such as water stored behind a dam. Kinetic energy is energy of motion, such as water rushing through a dam and downstream. Energy can be converted back and forth between potential and kinetic forms.

Energy Transformations in Chemical Bonds

Energy changes occur when chemical bonds are broken or formed. Breaking high‑energy bonds (for example, in glucose) and forming low‑energy bonds (as in carbon dioxide) releases kinetic energy that can do work or drive other processes.

The First and Second Laws of Thermodynamics

Energy is always conserved, but it changes in quality. The first law states that energy cannot be created or destroyed, only transformed. The second law states that energy tends to change from more‑ordered to less‑ordered forms as it is transformed, leading to increases in entropy over time. In practical terms, useful energy tends to become less usable as processes proceed, often dissipating as heat.

Real‑World Illustration: Energy in Firewood

Consider a log of firewood: it is highly organized and rich in potential energy. When burned, it releases carbon dioxide, water, and kinetic energy, while leaving behind ash with much lower useful energy. This example illustrates both energy transformation and the decline in usable energy quality over time.

Energy Sources and Efficiency

Some energy sources are easier to harness than others. Fossil fuels are highly concentrated and relatively easy to extract, whereas solar energy is diffuse and requires conversion devices to capture usable energy. The efficiency of energy conversions is a key measure: for example, a typical automobile engine uses about 16\% of the energy input to move the car, with the remainder lost as heat. This highlights how energy conversion efficiency shapes practical energy usage and environmental impact.

Solar Energy Powers Life

The sun emits energy across a broad electromagnetic spectrum, but atmospheric filtering allows primarily visible light to reach the surface. Organisms called autotrophs use the sun’s radiation directly to produce food through photosynthesis, converting water and carbon dioxide with solar energy into sugars with higher energy bonds.

Photosynthesis: From Light to Sugar

Photosynthesis occurs in chloroplasts, plant cell organelles, with chlorophyll acting as the primary pigment to drive the light reactions. During light reactions, water is split to produce hydrogen ions (H+), oxygen gas (O2), and high‑energy molecules ATP and NADPH, which fuel the subsequent Calvin cycle that builds sugars from carbon atoms. The overall process can be summarized by the equation: 6\,CO2 + 6\,H2O + \text{sun's energy} \rightarrow C6H{12}O6 + 6\,O2. Plants absorb water through their roots, take in carbon dioxide from the air through their leaves, and use sunlight to generate sugar and oxygen that support life on Earth.

Cellular Respiration: The Opposite Flow of Energy

Cellular respiration is essentially the reverse of photosynthesis: C6H{12}O6 + 6\,O2 \rightarrow 6\,CO2 + 6\,H2O. The energy released in respiration is about two‑thirds of the energy captured during photosynthesis, providing usable energy to both autotrophs and heterotrophs. This process occurs in all living organisms and is central to energy flow in ecosystems.

Geothermal Energy and Chemosynthesis

Beyond solar energy, Earth hosts geothermal energy arising from heat produced by radioactive decay deep within the planet. This heat slowly moves toward the surface, melts rock into magma, and can power plate tectonics. Hydrothermal vents on the ocean floor release jets of heated water, enabling organisms living nearby to use chemical potential energy contained in hydrogen sulfide (H₂S) to synthesize sugars via chemosynthesis. The chemosynthesis reaction is: 6\,CO2 + 6\,H2O + 3\,H2S \rightarrow C6H{12}O6 + 3\,H2SO4. This process supports unique ecosystems independent of sunlight and demonstrates the diversity of energy pathways in Earth's systems.

Connections to Foundational Principles and Real-World Implications

These notes connect fundamental concepts—matter, energy, atomic structure, bonding, and biochemical macromolecules—to large‑scale environmental phenomena and human activities. The Fukushima disaster underscores the persistence of contaminants and the importance of managing energy systems within ecological bounds. The conservation laws emphasize that while materials and energy can transform, their total quantity remains constant in closed contexts, guiding policy decisions about waste management and remediation. The dual roles of energy sources—from fossil fuels to solar and geothermal resources—highlight tradeoffs among energy density, accessibility, and environmental impact. Understanding photosynthesis and respiration clarifies why the Sun is the primary energy source for most ecosystems while also acknowledging alternative energy pathways like chemosynthesis in vent communities.