Atoms, Ions, and Molecules: Foundations for Anatomy & Physiology

Chapter 02: Atoms, Ions, and Molecules

Matter, Atoms, Elements, and the Periodic Table

Understanding the basic chemical principles is essential for studying anatomy and physiology. Matter is anything that has mass and occupies space, and it exists in three primary forms within the human body: solids, liquids, and gases.

• Solid: Example: bone

• Liquid: Example: blood

• Gas: Example: oxygen

An atom is the smallest particle that retains the chemical properties of an element. Elements are pure substances composed of only one type of atom, and they are organized in the periodic table of elements.

The Periodic Table of Elements

The periodic table arranges all known elements by increasing atomic number and groups them based on similar chemical properties. Each element is represented by a unique chemical symbol, atomic number, and average atomic mass.

• Atomic number: Number of protons in the nucleus

• Chemical symbol: One or two letters (e.g., C for carbon)

• Average atomic mass: Sum of protons and neutrons

Electronegativity increases from left to right across a row and from bottom to top in a column.

Common Elements of the Human Body

The human body is primarily composed of a few major elements, with several minor elements present in smaller quantities. These elements are essential for physiological processes.

Major Elements	% Body Weight	Minor Elements	% Body Weight
Oxygen (O)	65.0	Sulfur (S)	0.25
Carbon (C)	18.5	Potassium (K)	0.20
Hydrogen (H)	9.5	Sodium (Na)	0.15
Nitrogen (N)	3.0	Chlorine (Cl)	0.15
Calcium (Ca)	1.5	Magnesium (Mg)	0.05
Phosphorus (P)	1.0	Iron (Fe)	0.006

Major elements collectively compose almost 99% of body weight, while minor elements compose less than 1%.

Atomic Structure

Atoms consist of three subatomic particles:

• Protons: Positive charge (+1), mass of 1 atomic mass unit (amu), located in the nucleus

• Neutrons: No charge, mass of 1 amu, located in the nucleus

• Electrons: Negative charge (-1), mass of 1/1800 amu, located in electron orbitals surrounding the nucleus

The number of protons determines the atomic number and the identity of the element. Electrons occupy energy levels or shells around the nucleus, with each shell holding a specific number of electrons (first shell: 2, second shell: up to 8).

Determining Subatomic Particles

• Proton number = atomic number

• Neutron number = atomic mass - atomic number

• Electron number = proton number (in a neutral atom)

Example: Sodium (Na) has atomic number 11 and atomic mass 23. Neutron number = 23 - 11 = 12

Chemical Stability and the Octet Rule

Atoms tend to gain, lose, or share electrons to achieve a complete outer shell with eight electrons, known as the octet rule. Elements with a complete outer shell (e.g., noble gases) are stable and unreactive.

Ions and Ionic Compounds

Ions are atoms or molecules with a net electric charge due to the loss or gain of electrons.

• Cations: Positively charged ions (loss of electrons)

• Anions: Negatively charged ions (gain of electrons)

Ionic compounds are formed by the electrostatic attraction between cations and anions, resulting in a lattice structure (e.g., table salt, NaCl).

Covalent Bonding and Molecules

Covalent bonds involve the sharing of electrons between atoms. Molecules composed of different elements are called molecular compounds (e.g., CO2).

• Single covalent bond: One pair of electrons shared

• Double covalent bond: Two pairs of electrons shared

• Triple covalent bond: Three pairs of electrons shared

The number of covalent bonds an atom can form depends on the number of electrons needed to satisfy the octet rule (e.g., carbon forms four bonds).

Polar and Nonpolar Covalent Bonds

Electronegativity determines how electrons are shared in covalent bonds:

• Nonpolar covalent bond: Equal sharing of electrons (e.g., O2, C-H)

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

Electronegativity increases across the periodic table: Hydrogen < Carbon < Nitrogen < Oxygen.

Intermolecular Attractions

Weak chemical attractions between molecules, such as hydrogen bonds, are important for the structure and function of biological molecules (e.g., DNA, proteins).

• Hydrogen bond: Attraction between a partially positive hydrogen atom and a partially negative atom in another molecule

Molecular Structure and Properties of Water

Water is an inorganic molecule essential for life, making up two-thirds of body weight. Its molecular structure allows it to form hydrogen bonds, which are central to its unique properties.

• States of water: Gas (vapor), liquid, solid (ice)

• Functions: Transport, lubrication, cushioning, excretion

• Cohesion: Attraction between water molecules

• Surface tension: Inward pulling of cohesive forces at the surface

• Adhesion: Attraction between water and other substances

• High specific heat: Water resists temperature changes

• High heat of vaporization: Water requires much energy to change from liquid to gas

Water as the Universal Solvent

Water dissolves many substances, earning it the title "universal solvent." The chemical properties of a substance determine whether it will dissolve in water.

• Hydrophilic (water-loving): Polar molecules and ions dissolve in water

• Hydrophobic (water-fearing): Nonpolar molecules do not dissolve in water

Water can dissociate into ions, forming hydronium (H3O+) and hydroxide (OH-) ions, but remains neutral overall.

Acids, Bases, and pH

Acids dissociate in water to produce H+ ions (proton donors), increasing the concentration of free H+. Bases accept H+ ions (proton acceptors), decreasing the concentration of free H+.

• pH: Measures the relative amount of H+ in a solution, ranging from 0 (acidic) to 14 (basic)

• Neutralization: Acidic or basic solutions are returned to neutral by adding the opposite type

• Buffers: Help prevent pH changes by accepting or donating H+

Example equation for water dissociation: $\mathrm{H_2O} \rightleftharpoons \mathrm{H^+} + \mathrm{OH^-}$

Mixtures and Biological Macromolecules

Mixtures are combinations of substances that are not chemically bonded and can be separated physically. Biological macromolecules are large organic molecules essential for life, including carbohydrates, lipids, proteins, and nucleic acids.

• Carbohydrates: Energy source, structural components

• Lipids: Energy storage, membrane structure, hormones

• Proteins: Enzymes, structural support, movement, transport, protection

• Nucleic acids: Store and transfer genetic information

Macromolecules are formed by joining monomers through dehydration synthesis and broken down by hydrolysis.

Summary Table: Major Biological Macromolecules

Macromolecule	Monomer	Main Functions
Carbohydrates	Monosaccharides	Energy, structure
Lipids	Fatty acids, glycerol	Energy storage, membranes, hormones
Proteins	Amino acids	Enzymes, structure, movement, transport
Nucleic acids	Nucleotides	Genetic information

Example: Glucose is a monosaccharide and the primary energy source for cells. DNA is a nucleic acid that stores genetic information.

Additional info: These foundational chemical principles are essential for understanding the structure and function of cells, tissues, and organs in human anatomy and physiology.