Chapter 2: The Chemical Context of Life

Introduction to the Chemistry of Life

All living organisms are composed of matter, which is anything that occupies space and has mass. Understanding the chemical basis of life is essential for studying biology, as it explains how elements and compounds interact to form the molecules necessary for life.

Elements and Compounds

Elements

• Element: A substance that cannot be broken down into other substances by chemical reactions. Examples include carbon, oxygen, and gold.

• There are 92 naturally occurring elements, but only 20-25% are essential for life.

• Trace elements are required in very small amounts (e.g., iodine for thyroid function).

Compounds

• Compound: A substance consisting of two or more elements in a fixed ratio. Compounds have properties different from their constituent elements (emergent properties).

• Example: Table salt (NaCl) is composed of sodium (a metal) and chlorine (a gas), but together they form an edible compound.

Evolution of Tolerance to Toxic Elements

Some organisms have evolved to tolerate or even thrive in environments with toxic elements. For example, sunflowers can absorb heavy metals from contaminated soils, a process called phytoremediation.

Atomic Structure and Properties

Subatomic Particles

• Atoms are the smallest units of an element that retain its properties.

• Composed of protons (positive charge), neutrons (no charge), and electrons (negative charge).

• Protons and neutrons form the atomic nucleus; electrons orbit in shells around the nucleus.

Atomic Number and Atomic Mass

• Atomic number: Number of protons in the nucleus (defines the element).

• Mass number: Sum of protons and neutrons in the nucleus.

• Atomic mass: Approximated by the mass number.

• In a neutral atom, the number of protons equals the number of electrons.

Isotopes

• Isotopes: Atoms of the same element with different numbers of neutrons, resulting in different mass numbers.

• All isotopes of an element behave identically in chemical reactions.

• Radioactive isotopes have unstable nuclei that decay, emitting radiation. They are used in dating fossils, tracing metabolic pathways, and medical diagnostics (e.g., PET scans).

Energy Levels and Electron Shells

Energy and Electrons

• Energy: The capacity to cause change.

• Potential energy: Energy due to position or structure; electrons have more potential energy the farther they are from the nucleus.

• Electrons occupy electron shells with increasing energy levels as distance from the nucleus increases.

• Electrons can move between shells by absorbing or releasing energy.

Valence Electrons and Chemical Reactivity

• The valence shell is the outermost electron shell.

• Atoms with full valence shells are chemically inert (e.g., noble gases like helium, neon, argon).

• Atoms with incomplete valence shells are reactive and tend to form chemical bonds to achieve stability.

Chemical Bonds

Covalent Bonds

• Covalent bond: Sharing of a pair of valence electrons between two atoms.

• A single bond involves one pair of shared electrons; a double bond involves two pairs.

• Molecules are formed when two or more atoms are held together by covalent bonds.

Electronegativity and Polar Covalent Bonds

• Electronegativity: The tendency of an atom to attract electrons in a covalent bond.

• If atoms have different electronegativities, the electrons are shared unequally, resulting in a polar covalent bond.

• Nonpolar covalent bonds occur when electrons are shared equally.

Ionic Bonds

• Formed when one atom transfers an electron to another, creating oppositely charged ions (cation = positive, anion = negative).

• The electrostatic attraction between cations and anions forms an ionic bond.

• Ionic compounds are often called salts (e.g., NaCl).

Weak Chemical Interactions

• Hydrogen bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.

• Van der Waals interactions: Weak attractions due to transient local partial charges; important in large biological molecules and phenomena like gecko adhesion.

Chemical Reactions

Making and Breaking Bonds

• Chemical reactions involve the making and breaking of chemical bonds.

• Reactants are the starting materials; products are the resulting substances.

• Example: Photosynthesis

Properties of Water

Hydrogen Bonding in Water

• Water is a polar molecule with hydrogen bonds holding molecules together.

• Hydrogen bonding gives water unique properties essential for life.

Cohesion and Adhesion

• Cohesion: Water molecules stick to each other due to hydrogen bonding.

• Adhesion: Water molecules stick to other substances, aiding in water transport in plants.

Surface Tension

• Surface tension: The measure of how difficult it is to stretch or break the surface of a liquid.

• Water has high surface tension due to hydrogen bonding, allowing small organisms to walk on water.

Moderation of Temperature

• Water can absorb or release large amounts of heat with little temperature change, stabilizing environments and organisms.

Floating of Ice on Water

• Ice is less dense than liquid water because hydrogen bonds form a crystalline structure, causing ice to float.

• This property insulates aquatic life in cold climates.

Water as a Solvent

• Solution: A homogeneous mixture of substances.

• Solvent: The dissolving agent (water in aqueous solutions).

• Solute: The substance dissolved.

• Water dissolves ionic and polar substances due to its polarity.

Hydrophilic and Hydrophobic Substances

• Hydrophilic: Substances with an affinity for water (ionic or polar).

• Hydrophobic: Substances that repel water (nonpolar, e.g., oils).

Acids, Bases, and pH

Definitions and Importance

• Acids: Increase the concentration of H+ ions in solution (pH < 7).

• Bases: Decrease the concentration of H+ ions (pH > 7).

• Most biological fluids have a pH between 6 and 8; the internal pH of most living cells is close to 7.

• Buffers: Substances that minimize changes in pH by accepting or donating H+ ions as needed.

Additional info: Understanding the chemical context of life is foundational for all further study in biology, as it underpins the structure and function of biomolecules, cellular processes, and organismal physiology.