Atoms, Elements, and Chemical Bonds

Basic Concepts of Matter

Understanding the nature of matter is fundamental to biology, as all living things are composed of matter and its interactions.

• Matter: Anything that has mass and occupies space.

• Element: A pure substance consisting of only one type of atom; cannot be broken down by chemical means.

• Atom: The smallest unit of an element that retains its properties; cannot be broken down further by chemical means.

Atomic Structure

• Atomic Number: Number of protons in an atom; also equals the number of electrons in a neutral atom.

• Subatomic Particles:

  • Protons (p+): Positively charged, located in the nucleus.

  • Neutrons (n): Neutral charge, located in the nucleus.

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

• Electrons in the inner shell have the least amount of energy.

Elements Essential for Life

• 96% of the human body is composed of: Oxygen, Carbon, Hydrogen, Nitrogen.

• 3.7% are trace elements: Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, Magnesium.

Molecules and Compounds

• Molecule: Two or more atoms bonded together.

• Compound: Substance made of two or more different elements bonded together in a fixed ratio.

Chemical Bonds

Atoms combine through chemical bonds to form molecules and compounds. The type of bond affects the properties of the resulting substance.

• Covalent Bonds: Strongest; atoms share pairs of electrons.

  • Non-polar Covalent: Equal sharing of electrons (e.g., O2).

  • Polar Covalent: Unequal sharing of electrons, resulting in partial charges (e.g., H2O).

• Ionic Bonds: Middle strength; formed when electrons are transferred from one atom to another, creating ions.

• Hydrogen Bonds: Weakest; form between polar molecules where opposite partial charges attract (e.g., between water molecules).

Electronegativity

• The strength of an atom's attraction for electrons in a bond.

• Polar covalent bonds form between atoms with unequal electronegativity.

• Non-polar covalent bonds form between atoms with similar electronegativity.

Ions

• Cation: Positively charged ion (lost electrons).

• Anion: Negatively charged ion (gained electrons).

Chemical Reactions

• Reactants: Substances entering a reaction.

• Products: Substances produced by a reaction.

Water and Life

Properties of Water

Water's unique properties are essential for life and are largely due to its ability to form hydrogen bonds.

• Cohesion: Water molecules stick to each other via hydrogen bonds.

• Adhesion: Water molecules stick to other types of molecules.

• Surface Tension: Measure of how hard it is to break the surface of a liquid. Water has high surface tension due to hydrogen bonding.

• Ability to Moderate Temperature: Water absorbs and releases heat slowly, helping to stabilize temperatures.

• Expansion Upon Freezing: Water expands as it freezes, making ice less dense than liquid water.

• Versatility as a Solvent: Water dissolves many substances, making it the "universal solvent."

Types of Solutions

• Solution: Even mixture of solute and solvent.

• Solvent: Substance that dissolves another (e.g., water).

• Solute: Substance being dissolved.

• Aqueous Solution: Solution in which water is the solvent.

Hydrophobic and Hydrophilic Substances

• Hydrophobic: Substances that do not interact well with water (e.g., oils).

• Hydrophilic: Substances that interact well with water (e.g., salts, sugars).

Acids, Bases, and pH

• Acid: Substance that increases H+ concentration in solution.

• Base: Substance that increases OH- concentration or neutralizes acids.

• Buffer: Substance that minimizes changes in pH.

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

Formula:

Carbon and the Molecular Diversity of Life

Organic Chemistry

Organic chemistry is the study of carbon-containing compounds, which form the basis of all living organisms.

• Carbon atoms can form four covalent bonds, allowing for a diversity of stable structures.

• Carbon skeletons can vary in length, branching, double bond position, and ring structure.

• Hydrocarbons: Molecules consisting only of carbon and hydrogen; nonpolar and hydrophobic.

Functional Groups

Chemical groups attached to carbon skeletons determine the properties and reactivity of organic molecules.

• Examples: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl groups.

The Structure and Function of Large Biological Molecules

Macromolecules

Large biological molecules, or macromolecules, are essential for life and are built from smaller units called monomers.

• Monomer: Small molecule that can join with others to form a polymer.

• Polymer: Large molecule made of repeating monomers.

• Macromolecule: Very large polymer (e.g., proteins, nucleic acids).

Making and Breaking Polymers

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

• Hydrolysis: Breaks polymers apart by adding a water molecule.

• Enzymes: Specialized proteins that speed up chemical reactions.

Types of Macromolecules

• Carbohydrates: Simple sugars and polymers of sugars; provide energy and structural support.

• Lipids: Hydrophobic molecules including fats, phospholipids, and steroids; not true polymers.

• Proteins: Polymers of amino acids; perform a wide range of functions.

• Nucleic Acids: DNA and RNA; polymers of nucleotides; store and transmit genetic information.

Lipids

• Not true polymers.

• Mix poorly, if at all, with water.

• Consist mostly of hydrocarbon regions.

Fats

• Major function: energy storage.

• Constructed from glycerol and fatty acids.

• Glycerol: Three-carbon alcohol with a hydroxyl group attached to each carbon.

• Fatty Acid: Carboxyl group attached to a long carbon skeleton.

• Saturated Fatty Acid: No double bonds; solid at room temperature (most animal fats).

• Unsaturated Fatty Acid: One or more double bonds; causes kinks; liquid at room temperature (most plant and fish fats).

Phospholipids

• Major component of cell membranes.

• Composed of a phosphate head (hydrophilic) and two fatty acid tails (hydrophobic).

• Form bilayers in water, with hydrophilic heads facing outward and hydrophobic tails inward.

Steroids

• Lipids with a carbon skeleton of four fused rings.

• Distinguished by attached chemical groups (e.g., hormones like cholesterol).

Proteins

• Polymers of amino acids (20 types).

• Amino Acid: Contains an amino group, carboxyl group, and a unique side chain (R group).

• Polypeptide: Chain of amino acids.

• Protein: One or more polypeptides folded into a specific shape.

• Structure and function are sensitive to chemical and physical conditions (e.g., pH, temperature).

• Denaturation: Loss of protein structure due to environmental changes.

Nucleic Acids

• Store, transmit, and help express hereditary information.

• Polymers of nucleotides.

• Two types: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).

Functions of Nucleic Acids

• Store hereditary material.

• Transmit hereditary information.

• Help express hereditary information (instructions for protein synthesis).

Nitrogenous Bases

Base Pairing Rules

• DNA: A pairs with T, G pairs with C.

• RNA: A pairs with U, G pairs with C.

Structure of DNA and RNA

• DNA: Double helix; two polynucleotide strands spiral around an imaginary axis.

• RNA: Usually single-stranded; can form complementary pairing within or between molecules.