The Chemistry of Life: Foundations for General Biology

The Chemical Context of Life

Introduction to Chemical Elements and Compounds

All living organisms are composed of matter, which consists of chemical elements in pure form and in combinations called compounds. Understanding the properties and interactions of these elements is fundamental to biology.

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

• Compound: A substance consisting of two or more elements combined in a fixed ratio. Example: water (H2O), table salt (NaCl).

• Essential Elements: C, H, O, N make up about 96% of living matter. Trace elements are required in minute amounts (e.g., iron, iodine).

Atomic Structure and Properties

The properties of an element depend on the structure of its atoms, which are composed of subatomic particles:

• Protons: Positively charged particles in the nucleus; determine atomic number and element identity.

• Neutrons: Neutral particles in the nucleus; number can vary, forming isotopes.

• Electrons: Negatively charged particles orbiting the nucleus; involved in chemical bonding.

• Atomic Number: Number of protons in an atom.

• Mass Number: Sum of protons and neutrons.

• Isotopes: Atoms of the same element with different numbers of neutrons (e.g., 12C and 14C).

Chemical Bonds and Molecular Formation

Types of Chemical Bonds

Chemical bonds are interactions between the valence electrons of different atoms, resulting in molecule formation.

• Covalent Bonds: Atoms share pairs of electrons. Can be nonpolar (equal sharing, e.g., H2) or polar (unequal sharing, e.g., H2O).

• Ionic Bonds: Electrons are transferred from one atom to another, creating oppositely charged ions that attract (e.g., NaCl).

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom. Important in water and biological molecules.

• Van der Waals Interactions: Weak, transient attractions due to asymmetrical electron distribution.

Chemical Reactions

Chemical reactions make and break chemical bonds, converting reactants to products.

• General Equation:

$\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O}$

• Reactants: Starting materials.

• Products: Resulting substances.

• All chemical reactions are reversible.

Water and Life

Properties of Water

Hydrogen bonding gives water unique properties essential for life:

• Cohesion: Water molecules stick to each other via hydrogen bonds, contributing to surface tension and transport in plants.

• Adhesion: Water molecules stick to other substances (e.g., cell walls).

• Moderation of Temperature: Water has a high specific heat, allowing it to buffer temperature changes.

• Evaporative Cooling: As water evaporates, it removes heat, stabilizing temperatures in organisms and environments.

• Insulation by Ice: Ice is less dense than liquid water, so it floats, insulating bodies of water and protecting aquatic life.

• Solvent of Life: Water is a versatile solvent due to its polarity, dissolving many ionic and polar substances (hydrophilic), but not nonpolar substances (hydrophobic).

Acids, Bases, and pH

Acids and bases affect the pH of biological solutions, influencing cellular processes.

• Acid: Increases H+ concentration in solution (pH < 7).

• Base: Reduces H+ concentration (pH > 7).

• pH Scale: Ranges from 0 (acidic) to 14 (basic); pH 7 is neutral.

• Buffers: Substances that minimize pH changes by accepting or donating H+ ions. Example: carbonic acid (H2CO3) in blood.

Carbon and the Molecular Diversity of Life

Carbon's Unique Properties

Carbon is unparalleled in its ability to form diverse molecules due to its four valence electrons, allowing it to form up to four covalent bonds with a variety of atoms.

• Can form single, double, or triple bonds.

• Can form large, complex molecules with chains, rings, or branches.

Functional Groups

Functional groups are specific groups of atoms attached to carbon skeletons that confer distinct chemical properties to organic molecules.

Functional Group Name/Structure	Properties/Functions
Hydroxyl (–OH)	Alcohols; polar, can form hydrogen bonds, increases solubility in water
Carbonyl (–CO)	Ketones and aldehydes; found in sugars, can be structural isomers
Carboxyl (–COOH)	Carboxylic acids; acts as an acid, donates H+
Amino (–NH2)	Amines; acts as a base, picks up H+
Sulfhydryl (–SH)	Thiols; can form cross-links in proteins
Phosphate (–PO4)	Organic phosphates; contributes negative charge, can transfer energy
Methyl (–CH3)	Methylated compounds; affects gene expression

Macromolecules: Polymers and Monomers

Polymer Formation

Most biological macromolecules are polymers, long chains of repeating subunits called monomers.

• Dehydration Reaction: Joins monomers by removing a water molecule.

• Hydrolysis: Breaks polymers into monomers by adding water.

Example: Starch is a polymer of glucose; proteins are polymers of amino acids.

Carbohydrates: Fuel and Building Material

Carbohydrates include sugars and their polymers, serving as energy sources and structural materials.

• Monosaccharides: Simple sugars (e.g., glucose, fructose); formula is generally (CH2O)n.

• Disaccharides: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose).

• Polysaccharides: Polymers of monosaccharides; serve storage (starch, glycogen) or structural (cellulose, chitin) roles.

Example: Starch (plant storage), glycogen (animal storage), cellulose (plant cell walls).

Lipids: Diverse Hydrophobic Molecules

Types and Functions of Lipids

Lipids are a diverse group of hydrophobic molecules, including fats, phospholipids, and steroids.

• Fats: Composed of glycerol and fatty acids; store energy.

• Phospholipids: Major component of cell membranes; have hydrophilic heads and hydrophobic tails.

• Steroids: Lipids with a carbon skeleton of four fused rings (e.g., cholesterol).

Proteins and Nucleic Acids (Preview)

Proteins are polymers of amino acids with diverse functions, including catalysis, structure, and transport. Nucleic acids (DNA and RNA) store and transmit genetic information.

Additional info: This summary covers the foundational chemistry concepts essential for understanding biological molecules and processes, as outlined in introductory college biology courses.