The Chemical Basis of Life: Elements, Atoms, and Compounds

Chapter 2: The Chemical Basis of Life

Introduction

The study of biology is deeply connected to chemistry, as all living organisms are composed of chemical substances. Understanding the chemical basis of life is essential for explaining biological processes, such as how environmental changes can impact coral reefs. For example, when carbon dioxide (CO2) dissolves in water, it forms an acid that can disrupt the formation of coral skeletons.

Elements, Atoms, and Compounds

Elements and Compounds

All matter is composed of chemical elements, which are substances that cannot be broken down into other substances by chemical means. Living organisms are primarily made up of about 25 essential elements, with four elements—oxygen (O), carbon (C), hydrogen (H), and nitrogen (N)—making up about 96% of the mass of most living organisms.

• Element: A pure substance consisting of only one kind of atom.

• Compound: A substance formed when two or more different elements combine in a fixed ratio (e.g., water, H2O).

Compounds have properties different from the elements that compose them. For example, sodium (Na) and chlorine (Cl) combine to form sodium chloride (NaCl), or table salt.

Trace Elements

Trace elements are required by organisms in minute quantities but are essential for health. For example, fluoride is added to water and dental products to prevent tooth decay. Other trace elements are added to foods to preserve them, enhance nutrition, or improve appearance.

Atoms: Structure and Properties

Atomic Structure

An atom is the smallest unit of matter that retains the properties of an element. Atoms are composed of three types of subatomic particles:

• Protons (positively charged, located in the nucleus)

• Neutrons (neutral, located in the nucleus)

• Electrons (negatively charged, orbiting the nucleus)

The atomic number is the number of protons in an atom, which defines the element. The mass number is the sum of protons and neutrons in the nucleus. The atomic mass is approximately equal to the mass number.

Isotopes

Isotopes are atoms of the same element that have the same number of protons but different numbers of neutrons. Some isotopes are stable, while others are radioactive.

Isotope	Protons	Neutrons	Mass Number
Carbon-12	6	6	12
Carbon-13	6	7	13
Carbon-14	6	8	14

Chemical Bonds and Interactions

Electron Shells and Bonding

Electrons are arranged in electron shells around the nucleus. Atoms with incomplete outer shells tend to interact with other atoms, forming chemical bonds to achieve stability.

• Ionic bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other (e.g., NaCl).

• Covalent bonds: Formed when two atoms share one or more pairs of electrons. Covalent bonds can be nonpolar (equal sharing) or polar (unequal sharing).

• Hydrogen bonds: Weak bonds that occur when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom (common in water molecules).

Types of Covalent Bonds

• Nonpolar covalent bond: Electrons are shared equally between atoms (e.g., O2).

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges (e.g., H2O).

Ions and Ionic Compounds

An ion is an atom or molecule with an electrical charge due to the loss or gain of electrons. Ionic compounds, such as salts, are formed by the attraction between positive and negative ions.

Hydrogen Bonds

Hydrogen bonds are weak attractions between the slightly positive hydrogen atom of one molecule and the slightly negative atom of another molecule. These bonds are crucial in the structure and properties of water.

Chemical Reactions

Chemical reactions involve the breaking and forming of chemical bonds, resulting in the rearrangement of atoms. Reactants are transformed into products, but matter is neither created nor destroyed.

• Example: Formation of water from hydrogen and oxygen:

$2H_2 + O_2 \rightarrow 2H_2O$

Water: Life-Supporting Properties

Cohesion and Adhesion

Cohesion is the tendency of molecules of the same kind to stick together, while adhesion is the clinging of one substance to another. These properties contribute to surface tension and the formation of water droplets.

Temperature Moderation

Water has a high capacity to absorb and release heat with only slight temperature changes, due to hydrogen bonding. Evaporative cooling occurs when the surface of a liquid cools as water molecules evaporate.

Density of Ice

Water is less dense as a solid (ice) than as a liquid because hydrogen bonds form a stable, open structure when frozen. This causes ice to float on water, insulating aquatic life in cold environments.

Water as a Solvent

Water is known as the solvent of life because its polarity allows it to dissolve many substances, forming aqueous solutions. Polar or charged solutes are surrounded by water molecules, facilitating chemical reactions in cells.

Acids, Bases, and pH

The pH Scale

The pH scale measures the concentration of hydrogen ions (H+) in a solution, indicating how acidic or basic the solution is. A buffer is a substance that minimizes changes in pH.

• Acid: Substance that increases the H+ concentration.

• Base: Substance that decreases the H+ concentration.

Impact of Rising CO2 on Coral Reefs

Ocean Acidification

Rising atmospheric CO2 from fossil fuel combustion is absorbed by oceans, where it forms carbonic acid and lowers ocean pH—a process called ocean acidification. This reduces the availability of carbonate ions needed by corals and shell-building organisms for calcification.

As carbonate ion concentration decreases, the rate of calcium carbonate deposition by reef organisms slows, threatening coral growth and reef ecosystems.

Summary Table: Key Concepts

Concept	Definition	Example/Application
Element	Pure substance of one kind of atom	Oxygen (O), Carbon (C)
Compound	Substance of two or more elements in fixed ratio	Water (H2O)
Isotope	Atoms with same protons, different neutrons	Carbon-12, Carbon-14
Ionic Bond	Attraction between oppositely charged ions	NaCl (table salt)
Covalent Bond	Atoms share electrons	H2O, O2
Hydrogen Bond	Weak attraction between polar molecules	Between water molecules
pH	Measure of H+ concentration	pH 7 is neutral
Buffer	Minimizes pH changes	Bicarbonate in blood
Ocean Acidification	Decrease in ocean pH due to CO2	Threat to coral reefs

Additional info: This summary includes expanded academic context and definitions to ensure the notes are self-contained and suitable for exam preparation.