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, as all living organisms are composed of matter organized at the atomic and molecular levels.

• Matter: Anything that has mass and occupies space. It exists in three forms:

  • Solid (e.g., bone)

  • Liquid (e.g., blood)

  • Gas (e.g., oxygen)

• Atom: The smallest particle of an element that retains its chemical properties.

• Element: A pure substance consisting of only one type of atom. There are 92 naturally occurring elements, organized in the periodic table of elements.

The Periodic Table of Elements

The periodic table arranges elements by increasing atomic number and groups them based on similar chemical properties.

• Atomic number: Number of protons in the nucleus of an atom.

• Chemical symbol: One or two-letter abbreviation unique to each element (e.g., C for carbon).

• Average atomic mass: Sum of protons and neutrons, shown below the element's symbol.

• Electronegativity: Tendency of an atom to attract electrons, increases from left to right and bottom to top in the table.

Table: Most Common Elements of the Human Body

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%.

Components of an Atom

Atoms are composed of three subatomic particles:

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

• Neutrons: Mass of 1 amu, no charge, located in the nucleus.

• Electrons: Mass of 1/1800th amu, negative charge (-1), located in electron orbitals surrounding the nucleus.

Determining Subatomic Particles

• Proton number = atomic number

• Neutron number = atomic mass - atomic number

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

• Example: Sodium (Na): Atomic mass = 23, Atomic number = 11 Neutron number = 23 - 11 = 12

Atomic Structure and Electron Shells

Electrons occupy shells around the nucleus, each with a specific energy level and capacity:

• First shell: up to 2 electrons

• Second shell: up to 8 electrons

• Shells closest to the nucleus fill first

Chemical Stability and the Octet Rule

Atoms tend to lose, gain, or share electrons to achieve a complete outer shell of eight electrons (octet rule), making them stable and less reactive. Noble gases naturally have complete outer shells and are inert.

Ions and Ionic Compounds

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

• Cations: Positive charge (loss of electrons)

• Anions: Negative charge (gain of electrons)

• Polyatomic ions: Ions composed of more than one atom (e.g., bicarbonate HCO3-, phosphate PO43-)

Ionic bonds form between cations and anions, creating ionic compounds (e.g., NaCl, MgCl2).

Covalent Bonding, Molecules, and Molecular Compounds

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

• Molecular formula: Indicates number and type of atoms (e.g., H2O)

• Structural formula: Shows arrangement of atoms (e.g., O=C=O for CO2)

• Isomers: Molecules with the same molecular formula but different structures and properties (e.g., glucose, galactose, fructose)

Types of Covalent Bonds

• Single covalent bond: One pair of electrons shared

• Double covalent bond: Two pairs of electrons shared

• Triple covalent bond: Three pairs of electrons shared

Polarity in Covalent Bonds

Electronegativity determines how electrons are shared:

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

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

Most common elements in living organisms, from least to greatest electronegativity: Hydrogen < Carbon < Nitrogen < Oxygen.

Nonpolar, Polar, and Amphipathic Molecules

• Nonpolar molecules: Contain nonpolar covalent bonds (e.g., O2, C-H)

• Polar molecules: Contain polar covalent bonds (e.g., H2O)

• Amphipathic molecules: Contain both polar and nonpolar regions (e.g., phospholipids)

Intermolecular Attractions

• Hydrogen bonds: Weak attractions between partially positive hydrogen and partially negative atoms in polar molecules; important for the structure of water, DNA, and proteins.

Molecular Structure and Properties of Water

Water is an inorganic molecule essential for life, making up two-thirds of human body weight.

• Composed of one oxygen atom bonded to two hydrogen atoms

• Oxygen has partial negative charges; hydrogens have partial positive charges

• Can form up to four hydrogen bonds with adjacent molecules

Properties of Water

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

• Functions: Transports substances, lubricates, cushions, excretes wastes

• Cohesion: Attraction between water molecules

• Surface tension: Inward pulling at the surface due to cohesion

• Adhesion: Attraction between water and other substances

• High specific heat: Water resists temperature changes; $C = \frac{q}{m \Delta T}$

• High heat of vaporization: Requires significant energy to change from liquid to gas

Water as the Universal Solvent

• Solvent: Substance that dissolves solutes; water is called the universal solvent

• Hydrophilic: Substances that dissolve in water (e.g., glucose, salts)

• Hydrophobic: Substances that do not dissolve in water (e.g., fats, cholesterol)

• Electrolytes: Substances that dissociate in water and conduct electricity (e.g., NaCl)

• Nonelectrolytes: Substances that dissolve but do not dissociate or conduct electricity

Water: A Neutral Solvent

• Water can spontaneously dissociate to form ions: $2H_2O \rightleftharpoons H_3O^+ + OH^-$

• Equal numbers of H+ and OH- ions keep water neutral (pH = 7)

Acids and Bases

• Acid: Dissociates in water to produce H+ (proton donor), increases H+ concentration

• Base: Accepts H+ (proton acceptor), decreases H+ concentration

• Strong acids/bases: Dissociate/absorb H+ completely

• Weak acids/bases: Dissociate/absorb H+ partially

pH, Neutralization, and Buffers

• pH: Measures H+ concentration; scale from 0 (acidic) to 14 (basic)

• pH and H+ concentration are inversely related: $pH = -\log[H^+]$

• Neutralization: Acidic or basic solutions returned to neutral (pH 7)

• Buffers: Help prevent pH changes by accepting or donating H+ (e.g., carbonic acid-bicarbonate buffer in blood)

Water Mixtures

• Suspension: Large particles, settle out unless in motion (e.g., blood cells in plasma)

• Colloid: Medium particles, remain mixed, scatter light (e.g., plasma proteins)

• Solution: Small particles, dissolve completely, do not scatter light (e.g., salt water)

• Emulsion: Special colloid of water and nonpolar liquid (e.g., oil and vinegar)

Biological Macromolecules: General Characteristics

• Large organic molecules synthesized by the body

• Contain carbon, hydrogen, oxygen; may include nitrogen, phosphorus, sulfur

• Composed of monomers (repeating subunits)

• Bonded by dehydration synthesis (removal of water), broken by hydrolysis (addition of water)

Lipids

• Diverse group of nonpolar, water-insoluble molecules

• Functions: Energy storage, membrane structure, hormones

• Classes: Triglycerides (energy storage), Phospholipids (membranes), Steroids (hormones), Eicosanoids (signaling)

• Triglycerides: Glycerol + 3 fatty acids; saturated (no double bonds), unsaturated (one or more double bonds)

• Phospholipids: Amphipathic, with hydrophilic head and hydrophobic tails

• Steroids: Four-ring structure (e.g., cholesterol, hormones)

Carbohydrates

• General formula: (CH2O)n

• Monosaccharides: Simple sugars (e.g., glucose)

• Disaccharides: Two monosaccharides (e.g., sucrose, lactose)

• Polysaccharides: Many monosaccharides (e.g., glycogen, starch, cellulose)

• Glycogen: Storage form of glucose in animals

Nucleic Acids

• Store and transfer genetic information

• Polymers of nucleotide monomers

• DNA: Double-stranded, deoxyribose sugar, bases: adenine, guanine, cytosine, thymine

• RNA: Single-stranded, ribose sugar, bases: adenine, guanine, cytosine, uracil

• ATP: Adenosine triphosphate, energy transfer molecule

Proteins

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

• Polymers of amino acids (20 types)

• Structure: Amine group, carboxyl group, hydrogen, and R group

• Primary structure: Linear sequence of amino acids

• Denaturation: Loss of protein structure and function due to temperature or pH changes

Example: Hemoglobin is a protein that transports oxygen in the blood; its function depends on its precise amino acid sequence and three-dimensional structure.