Chapter 2: The Chemical Context of Life

Concept 2.1: Matter, Elements, and Compounds

Matter is anything that has mass and occupies space. All living organisms are composed of matter, which is made up of chemical elements. Elements are substances that cannot be broken down into other substances by chemical reactions. Compounds are substances consisting of two or more elements combined in a fixed ratio.

• Matter: Composed of elements in pure form or in combinations called compounds.

• Element: A substance that cannot be broken down by chemical means.

• Compound: A substance consisting of two or more elements in a fixed ratio.

• Example: Table salt (NaCl) is a compound of sodium and chlorine.

Chemical Composition of the Human Body

The human body is primarily composed of a few key elements. These elements are essential for life and make up the majority of living matter.

• Major elements: Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N), Calcium (Ca), and Phosphorus (P) make up about 99% of the human body.

• Trace elements: Potassium (K), Sulfur (S), Sodium (Na), Chlorine (Cl), Magnesium (Mg), and others are present in smaller amounts but are still essential for life.

Concept 2.2: Atomic Structure and Properties

Atoms and Subatomic Particles

An atom is the smallest unit of matter that retains the properties of an element. Atoms are composed of subatomic particles: protons, neutrons, and electrons.

• Protons: Positively charged particles found in the nucleus; determine the element.

• Neutrons: Neutral particles found in the nucleus; determine the isotope.

• Electrons: Negatively charged particles that orbit the nucleus; determine chemical behavior.

Atomic Number, Mass Number, and Atomic Mass

Atoms of different elements differ in their number of subatomic particles. The atomic number is the number of protons in the nucleus, while the mass number is the sum of protons and neutrons. Atomic mass is the average mass of all isotopes of an element, weighted by their natural abundance.

• Atomic Number (Z): Number of protons in the nucleus.

• Mass Number (A): Number of protons plus neutrons.

• Atomic Mass: Weighted average of all isotopes of an element.

Isotopes and Radioactivity

Isotopes are atoms of the same element that differ in the number of neutrons. Some isotopes are unstable (radioactive) and decay spontaneously, emitting particles and energy.

• Isotope: Atoms of the same element with different numbers of neutrons.

• Radioactive Isotope: An isotope that decays spontaneously, releasing radiation.

Energy Levels and Electron Shells

Electrons have potential energy due to their position relative to the nucleus. They occupy specific energy levels, or shells, with electrons in higher shells having more energy. When electrons absorb energy, they move to higher shells; when they lose energy, they fall to lower shells.

• Electron Shells: Energy levels where electrons are found.

• Valence Electrons: Electrons in the outermost shell, important for chemical bonding.

Electron Distribution and the Periodic Table

The chemical behavior of an atom is determined by the distribution of electrons in its shells, especially the valence shell. The periodic table arranges elements by increasing atomic number and groups elements with similar chemical properties together.

• First shell: Maximum 2 electrons

• Second and third shells: Maximum 8 electrons each

• Fourth shell: Maximum 18 electrons

Electron Orbitals

Orbitals are three-dimensional spaces where electrons are found 90% of the time. Each shell contains a specific number of orbitals, and each orbital can hold up to two electrons.

• 1s orbital: Spherical shape, holds 2 electrons

• 2s and 2p orbitals: 2s is spherical, 2p are dumbbell-shaped, each holds 2 electrons

Concept 2.3: Chemical Bonds and Molecular Structure

Chemical Bonds: Covalent, Ionic, and Weak Interactions

Atoms with incomplete valence shells can share or transfer electrons, forming chemical bonds. The main types of bonds are covalent, ionic, hydrogen bonds, and van der Waals interactions.

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

• Ionic Bond: Transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

• Hydrogen Bond: Attraction 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.

Covalent Bonds

• Single Bond: Sharing of one pair of electrons (e.g., H—H).

• Double Bond: Sharing of two pairs of electrons (e.g., O═O).

• Electronegativity: The attraction of an atom for electrons in a covalent bond. Higher electronegativity means stronger pull on electrons.

• Nonpolar Covalent Bond: Electrons are shared equally.

• Polar Covalent Bond: Electrons are shared unequally, creating partial charges.

Ionic Bonds

• Cation: Positively charged ion (loses electrons).

• Anion: Negatively charged ion (gains electrons).

• Ionic Compound: Compound formed by ionic bonds, often called a salt (e.g., NaCl).

Weak Chemical Interactions

• Hydrogen Bonds: Important in stabilizing the structures of proteins and DNA.

• Van der Waals Interactions: Weak attractions that can be significant in large numbers, such as in gecko toe adhesion.

Molecular Shape and Function

The shape of a molecule is determined by the positions of its atoms' orbitals and is crucial for its function. Molecular shape determines how biological molecules recognize and interact with each other, such as hormones binding to receptors.

• Hybridization of Orbitals: s and p orbitals may hybridize, creating specific shapes (e.g., tetrahedral).

• Biological Recognition: Molecules with similar shapes can bind to the same receptors (e.g., morphine and endorphins).

Concept 2.4: Chemical Reactions

Chemical Reactions and Equilibrium

Chemical reactions involve the making and breaking of chemical bonds. Reactants are the starting materials, and products are the resulting substances. All chemical reactions are reversible, and equilibrium is reached when the forward and reverse reactions occur at the same rate.

• Reactants: Starting substances in a chemical reaction.

• Products: Substances formed from a chemical reaction.

• Chemical Equilibrium: State where the concentrations of reactants and products remain constant.

Photosynthesis: An Example of a Chemical Reaction

Photosynthesis is a key chemical reaction in biology, converting carbon dioxide and water into glucose and oxygen using sunlight.

• Equation:

• Importance: Provides energy and organic molecules for living organisms.