Water and Carbon: The Chemical Basis of Life

Introduction to Chemical Evolution

Chemical evolution is the leading scientific explanation for the origin of life on Earth. It describes the process by which simple chemical substances formed increasingly complex carbon-containing molecules, eventually leading to the first self-replicating molecules and the transition to biological evolution.

• Chemical evolution: The process by which inorganic molecules gave rise to complex organic molecules.

• Biological evolution: Began when molecules could replicate, leading to natural selection and the emergence of life’s five characteristics (replication, metabolism, cells, information, and evolution).

• Example: The formation of RNA-like molecules capable of self-replication.

Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution

Major Elements in Living Organisms

Four types of atoms make up about 96% of the matter in living organisms: hydrogen (H), carbon (C), nitrogen (N), and oxygen (O). These elements are fundamental to the structure and function of biological molecules.

• Hydrogen, carbon, nitrogen, oxygen: Most abundant elements in cells.

• Other elements: Phosphorus (P) and sulfur (S) are also important but less abundant.

Basic Atomic Structure

Atoms are composed of three subatomic particles: protons, neutrons, and electrons.

• Protons: Positively charged (+1), found in the nucleus.

• Neutrons: Neutral charge, also in the nucleus.

• Electrons: Negatively charged (-1), orbit the nucleus in electron shells.

• Atoms are electrically neutral when the number of protons equals the number of electrons.

Atomic Number and Mass Number

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

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

• Isotopes: Atoms of the same element with different numbers of neutrons (different mass numbers).

• Atomic weight: Average mass of all naturally occurring isotopes of an element, weighted by abundance.

Electron Arrangement and Chemical Behavior

The arrangement of electrons in shells and orbitals determines how atoms interact and form bonds.

• Electron shells: Energy levels where electrons are found; shells closer to the nucleus are lower in energy.

• Orbitals: Regions within shells where electrons are likely to be found; each orbital holds up to two electrons.

• Valence shell: Outermost electron shell; electrons here are called valence electrons and determine chemical reactivity.

• Valence: Number of unpaired valence electrons; indicates how many bonds an atom can form.

Chemical Bonds

Atoms form chemical bonds to achieve full valence shells, resulting in more stable configurations.

• Covalent bonds: Atoms share pairs of valence electrons. Molecules are formed by covalent bonding.

• Nonpolar covalent bonds: Electrons are shared equally (e.g., C–H bond).

• Polar covalent bonds: Electrons are shared unequally due to differences in electronegativity (e.g., O–H bond in water).

• Ionic bonds: Electrons are transferred from one atom to another, creating charged ions (cations and anions) that attract each other.

Electronegativity and Bond Polarity

• Electronegativity: The ability of an atom to attract electrons in a bond. Increases across a period and up a group in the periodic table.

• Partial charges: In polar covalent bonds, the more electronegative atom gains a partial negative charge (δ−), while the less electronegative atom gains a partial positive charge (δ+).

• Example: In water (H2O), oxygen is more electronegative than hydrogen, resulting in a polar molecule.

Representation of Molecules

• Molecular formulas: Indicate the types and numbers of atoms (e.g., H2O, CH4).

• Structural formulas: Show how atoms are bonded and the types of bonds (single, double, triple).

• Ball-and-stick and space-filling models: Illustrate the three-dimensional geometry of molecules.

Properties of Water and Its Importance to Life

Water as a Solvent

Water is an excellent solvent due to its polarity and ability to form hydrogen bonds.

• Solvent: The substance in which solutes dissolve to form a solution.

• Hydrophilic substances: Ions and polar molecules that dissolve easily in water due to interactions with water’s partial charges.

• Hydrophobic substances: Nonpolar molecules that do not dissolve in water; they cluster together via hydrophobic interactions and van der Waals forces.

Hydrogen Bonding

• Hydrogen bonds: Weak electrical attractions between the partial positive charge on a hydrogen atom and the partial negative charge on another atom (often oxygen or nitrogen).

• Responsible for many of water’s unique properties.

Cohesion, Adhesion, and Surface Tension

• Cohesion: Attraction between like molecules (water to water), leading to surface tension.

• Adhesion: Attraction between unlike molecules (water to other substances).

• Surface tension: The cohesive force at the surface of water that makes it behave like an elastic membrane.

• Example: Water moving up plant stems against gravity due to cohesion and adhesion.

Density and States of Water

• Water is denser as a liquid than as a solid (ice), because ice forms an open crystal structure due to hydrogen bonding.

• This property allows ice to float, insulating aquatic environments.

Thermal Properties of Water

• Specific heat: The amount of energy required to raise the temperature of 1 gram of a substance by 1°C.

• Water has a high specific heat due to hydrogen bonding, which buffers temperature changes.

• Heat of vaporization: The energy required to convert 1 gram of liquid water to gas. Water’s high heat of vaporization makes sweating an effective cooling mechanism.

Acids, Bases, and pH

Acid-Base Reactions in Water

• Acid: Substance that donates protons (H+) and increases hydronium ion (H3O+) concentration.

• Base: Substance that accepts protons and decreases hydronium ion concentration.

• Water dissociation:

• In reality, protons associate with water to form hydronium ions:

pH Scale

• pH: A measure of hydrogen ion concentration;

• Acidic solutions: pH < 7

• Basic solutions: pH > 7

• Neutral: pH = 7 (pure water)

• Buffers: Substances that minimize changes in pH, helping maintain homeostasis in organisms.

Concentration and Moles

• Mole: 6.022 × 1023 particles (Avogadro’s number).

• Molecular weight: Sum of atomic weights of all atoms in a molecule.

• Molarity (M): Number of moles of solute per liter of solution.

Carbon: The Backbone of Life

Properties of Carbon

• Carbon forms four covalent bonds, allowing for a variety of stable, complex molecules.

• Organic compounds: Molecules containing carbon bonded to other elements (H, N, O, P, S).

• Carbon skeletons can form chains, rings, and branched structures.

Functional Groups in Organic Molecules

• Amino group (–NH2): Acts as a base, attracts protons.

• Carboxyl group (–COOH): Acts as an acid, donates protons.

• Carbonyl group (–C=O): Important in linking molecules together.

• Hydroxyl group (–OH): Acts as a weak acid.

• Phosphate group (–PO42−): Has two negative charges, important in energy transfer.

• Sulfhydryl group (–SH): Can form disulfide bonds, stabilizing protein structure.

Macromolecules and Polymerization

• Macromolecules: Large molecules made of smaller subunits (monomers) joined by covalent bonds.

• Polymerization: Process of linking monomers to form polymers, often via condensation (dehydration) reactions (loss of water).

• Hydrolysis: Breaking polymers into monomers by adding water; increases entropy and is energetically favorable.

• Examples: Proteins, nucleic acids, and carbohydrates are biological macromolecules formed by polymerization.