Chapter 2: The Chemical Context of Life

Concept 2.1: Matter Consists of Chemical Elements in Pure Form and in Combinations Called Compounds

All living organisms are composed of matter, which is anything that occupies space and has mass. Matter is organized into elements and compounds, each with distinct properties essential for life.

• Matter: Anything that takes up space and has mass.

• Element: A substance that cannot be broken down into other substances by chemical reactions.

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

• Emergent Properties: New characteristics that arise when elements combine to form compounds (e.g., table salt, NaCl, has properties different from sodium and chlorine alone).

The Elements of Life

Of the 92 naturally occurring elements, only a small subset is essential for life. These elements are required in varying amounts by living organisms.

• Essential Elements: About 20–25% of elements are required for life. The four main elements—carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)—make up approximately 96% of living matter.

• Other important elements include calcium (Ca), phosphorus (P), potassium (K), and sulfur (S).

• Trace Elements: Elements required in minute quantities (e.g., iron, iodine).

Additional info: Table values are representative and may vary slightly by source.

Concept 2.2: An Element’s Properties Depend on the Structure of Its Atoms

Atoms are the smallest units of matter that retain the properties of an element. The structure of atoms determines the chemical behavior of elements.

• Atom: Composed of subatomic particles: neutrons (no charge), protons (positive charge), and electrons (negative charge).

• Neutrons and protons are located in the atomic nucleus; electrons form a "cloud" around the nucleus.

• Proton and neutron mass ≈ 1 dalton; electron mass is negligible.

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: Approximate total mass of an atom (measured in daltons).

Isotopes

• Atoms of the same element with different numbers of neutrons are called isotopes.

• Radioactive Isotopes: Unstable isotopes that decay spontaneously, emitting particles and energy.

The Energy Levels of Electrons

• Energy: The capacity to cause change; potential energy is energy due to position or structure.

• Electrons have different potential energies depending on their distance from the nucleus.

• Electrons occupy electron shells with characteristic energy levels.

Electron Distribution and Chemical Properties

• The arrangement of electrons in shells determines an atom’s chemical behavior.

• The periodic table arranges elements by increasing atomic number and electron configuration.

• Valence Electrons: Electrons in the outermost shell; determine chemical reactivity.

• Elements with full valence shells are chemically inert (e.g., noble gases).

Electron Orbitals

• Orbital: A three-dimensional space where an electron is found 90% of the time.

• Each shell contains a specific number of orbitals; each orbital holds up to 2 electrons.

• Atoms interact to complete their valence shells, often forming chemical bonds.

Concept 2.3: The Formation and Function of Molecules and Ionic Compounds Depend on Chemical Bonding Between Atoms

Atoms with incomplete valence shells can share or transfer electrons, forming chemical bonds that hold atoms together in molecules or compounds.

Covalent Bonds

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

• Single Bond: Sharing of one pair of electrons; Double Bond: Sharing of two pairs.

• Structural Formula: Shows arrangement of atoms and bonds (e.g., H—H for hydrogen gas).

• Molecular Formula: Indicates the number and type of atoms (e.g., H2O).

• Valence: Bonding capacity of an atom, usually equal to the number of unpaired electrons in the valence shell.

• Electronegativity: Atom’s attraction for shared electrons in a covalent bond.

• Nonpolar Covalent Bond: Electrons shared equally (e.g., H2).

• Polar Covalent Bond: Electrons shared unequally, resulting in partial charges (e.g., H2O).

Ionic Bonds

• Formed when one atom transfers electrons to another, creating ions.

• Cation: Positively charged ion; Anion: Negatively charged ion.

• Ionic Bond: Attraction between oppositely charged ions.

• Ionic Compounds (Salts): Compounds formed by ionic bonds (e.g., NaCl). Often form crystalline structures and dissociate easily in water.

Weak Chemical Interactions

• Most strong bonds in organisms are covalent, but weak interactions are crucial for biological function.

• Weak bonds are reversible, allowing dynamic molecular interactions.

Hydrogen Bonds

• Form when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom (commonly O or N).

Van der Waals Interactions

• Weak attractions between molecules due to transient local partial charges.

• Collectively, these interactions can be significant (e.g., gecko’s toe hairs adhering to surfaces).

Molecular Shape and Function

• Molecular shape is determined by the positions of atoms’ orbitals and is critical for function.

• Shape determines how molecules recognize and interact with each other (e.g., opiates and endorphins binding to brain receptors).

Concept 2.4: Chemical Reactions Make and Break Chemical Bonds

Chemical reactions involve the making and breaking of chemical bonds, transforming reactants into products.

• Reactants: Starting materials in a chemical reaction.

• Products: Resulting materials after the reaction.

• All chemical reactions are reversible; products can become reactants in the reverse reaction.

• Chemical Equilibrium: State where forward and reverse reactions occur at the same rate, and concentrations of reactants and products remain constant.

Example: Photosynthesis

• Sunlight powers the conversion of carbon dioxide and water into glucose and oxygen.

Additional info: Chemical equilibrium does not mean equal concentrations, but rather stable ratios of reactants and products.