Atoms, Ions, and Molecules: Chemical Foundations of Anatomy & Physiology

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Atoms, Ions, and Molecules

Introduction to Matter in the Human Body

The human body is composed of matter, which exists in three primary forms: solids, liquids, and gases. Understanding the chemical nature of matter is essential for studying anatomy and physiology.

Solid: Example – bone
Liquid: Example – blood
Gas: Example – oxygen

Matter is made up of atoms, the smallest units that retain the properties of an element. Elements are organized in the periodic table of elements.

Elements of the Human Body

Elements are pure substances consisting of only one type of atom. The human body is primarily composed of a few key elements, each with specific biological roles.

Element	% of Total Body Mass	Significance
Oxygen (O)	65.0	Part of water and many organic molecules; used to generate ATP, the energy currency of cells.
Carbon (C)	18.5	Forms backbone chains and rings of all organic molecules: carbohydrates, lipids, proteins, nucleic acids.
Hydrogen (H)	9.5	Constituent of water and most organic molecules; ionized form (H+) makes body fluids acidic.
Nitrogen (N)	3.2	Component of all proteins and nucleic acids.

Additional info: Other elements such as calcium, phosphorus, potassium, sulfur, sodium, chlorine, magnesium, and iron are present in smaller amounts but are essential for various physiological functions.

Atomic Structure

Subatomic Particles

Atoms are composed of three main subatomic particles:

Protons: Positive charge (+1), located in the nucleus.
Neutrons: No charge, located in the nucleus.
Electrons: Negative charge (-1), located in electron shells around the nucleus.

The atomic number is the number of protons in an atom and defines the element. In a neutral atom, the number of electrons equals the number of protons.

Mass Number and Isotopes

Mass Number: The sum of protons and neutrons in the nucleus.
Isotopes: Atoms of the same element with the same number of protons but different numbers of neutrons. Isotopes have nearly identical chemical properties.

Example: Carbon has three isotopes: Carbon-12 (6 neutrons), Carbon-13 (7 neutrons), and Carbon-14 (8 neutrons).

Ions and Molecules

Ions

An ion is an atom or molecule with a net electric charge due to the loss or gain of electrons.

Cation: Positively charged ion (loss of electrons).
Anion: Negatively charged ion (gain of electrons).

Common Ions in the Body

Cations	Symbol	Anions	Symbol
Hydrogen ion	H+	Fluoride ion	F-
Sodium ion	Na+	Chloride ion	Cl-
Potassium ion	K+	Iodide ion	I-
Ammonium ion	NH4+	Hydroxide ion	OH-
Magnesium ion	Mg2+	Bicarbonate ion	HCO3-
Calcium ion	Ca2+	Oxide ion	O2-
Iron (II) ion	Fe2+	Sulfate ion	SO42-
Iron (III) ion	Fe3+	Phosphate ion	PO43-

Molecules and Chemical Bonds

Molecule: Two or more atoms sharing electrons.
Ionic Bond: Formed when cations and anions attract each other (e.g., NaCl).
Covalent Bond: Formed when atoms share electrons. Can be single, double, or triple bonds; more shared pairs mean a stronger bond.

Example: Water (H2O) is a covalently bonded molecule.

Chemical Reactions and Energy

Chemical Reactions

A chemical reaction occurs when new bonds are formed or old bonds are broken. The substances present at the start are reactants, and those formed are products.

Metabolism: The sum of all chemical reactions in the body.

Energy in Chemical Reactions

Energy: The capacity to do work.
Potential Energy: Stored energy due to position or structure.
Kinetic Energy: Energy of motion.
Chemical Energy: A form of potential energy stored in chemical bonds.

Energy Transfer and Reaction Types

Exergonic Reactions: Release more energy than they absorb.
Endergonic Reactions: Absorb more energy than they release.
Activation Energy: The minimum energy required to start a reaction.
Catalysts: Substances (often enzymes) that lower activation energy and speed up reactions without being consumed.

Types of Chemical Reactions

Synthesis: Atoms or molecules combine to form larger molecules.
Decomposition: Large molecules are broken down into smaller components.
Exchange: Involve both synthesis and decomposition.
Reversible: Products can revert to reactants.
Oxidation-Reduction: Involve transfer of electrons between atoms/molecules.

Water and Solutions

Water as the Universal Solvent

Water is the main solvent in the body, dissolving many substances (solutes). Its chemical properties determine what will dissolve:

Hydrophilic: Substances that dissolve in water (polar molecules).
Hydrophobic: Substances that do not dissolve in water (nonpolar molecules).

Thermal Properties of Water

High heat capacity (absorbs and releases heat slowly).
High heat of vaporization (requires much energy to change from liquid to gas).
Acts as a lubricant, reducing friction between body structures.

Acids, Bases, and pH

Definitions

Acid: Dissociates in water to produce H+; proton donor; increases H+ concentration.
Base: Accepts H+; proton acceptor; decreases H+ concentration.
pH: A measure of H+ concentration, expressed as a number from 0 to 14. Lower pH = higher H+ (more acidic); higher pH = lower H+ (more basic).

The pH of pure water is 7 (neutral).

pH Scale Examples

Hydrochloric acid: pH 0
Gastric juice: pH 1-2
Grape juice: pH 3
Milk, saliva: pH 6.3-6.6
Pure water: pH 7
Household ammonia: pH 11
Sodium hydroxide: pH 14

Organic Compounds

General Properties

Always contain carbon.
Can form various shapes and structures.
Often do not dissolve easily in water.
Serve as a major energy source.

Major Classes of Organic Compounds

Carbohydrates: Provide most of the energy needed for life.
Lipids: Diverse group of hydrophobic molecules; provide protection, insulation, and energy.
Proteins: Composed of amino acids; provide structure, regulate processes, assist in muscle contraction, transport substances, and serve as enzymes.
Nucleic Acids: DNA and RNA; store and transmit genetic information.

Carbohydrates

Monosaccharides: Simple sugars (e.g., glucose).
Disaccharides: Two monosaccharides joined (e.g., sucrose, lactose, maltose).
Polysaccharides: Many monosaccharides joined (e.g., glycogen in animals, starch and cellulose in plants).

Glucose is the most common monosaccharide and the primary energy source for cells. Excess glucose is stored as glycogen in the liver and skeletal muscle.

Lipids

Triglycerides: Most common lipid; used for long-term energy storage, insulation, and protection.
Phospholipids: Major component of cell membranes.
Steroids: Include hormones and bile salts.

Proteins

Composed of amino acid monomers (20 types in living organisms).
Form polymers: dipeptides, tripeptides, polypeptides.
Functions: structure, regulation, protection, muscle contraction, transport, enzymes.

Protein Structure:

Primary: Sequence of amino acids.
Secondary: Local folding (e.g., alpha-helix, beta-sheet).
Tertiary: Overall 3D shape.
Denaturation: Loss of structure and function due to heat or chemicals; often irreversible.

Enzymes

Proteins that act as biological catalysts.
Highly specific, extremely efficient, and regulated by the cell.
Names often end in -ase.

Nucleic Acids

DNA (Deoxyribonucleic Acid): Double-stranded; stores genetic information; found in the nucleus and mitochondria; bases: adenine, guanine, cytosine, thymine.
RNA (Ribonucleic Acid): Single-stranded; involved in protein synthesis; found in nucleus and cytoplasm; bases: adenine, guanine, cytosine, uracil.

Adenosine Triphosphate (ATP)

ATP is the principal energy-storing molecule in the body. It consists of adenosine (adenine + ribose) and three phosphate groups. The breakdown of ATP releases energy for cellular processes.

Used for muscle contraction, movement of chromosomes, transport across membranes, and synthesis of molecules.

ATP Cycle:

ATP is broken down to ADP (adenosine diphosphate) and a phosphate group, releasing energy.
ADP can be converted back to ATP using energy from food.

Additional info: Enzymes control the synthesis and breakdown of ATP, making it a renewable energy source for the cell.