Atoms, Molecules, and Chemical Foundations in Anatomy & Physiology

Atomic Structure and Elements

Basic Structure of the Atom

Atoms are the fundamental units of matter, composed of a central nucleus and an electron cloud. Understanding atomic structure is essential for grasping chemical interactions in biological systems.

• Nucleus: Contains protons (positive charge) and neutrons (no charge).

• Electron cloud: Surrounds the nucleus; contains electrons (negative charge).

• Elements: Pure substances consisting of only one type of atom (e.g., Carbon (C), Nitrogen (N), Oxygen (O)).

Model of the Atom

The atom consists of a nucleus with protons and neutrons, surrounded by electrons in defined energy levels or shells.

• Protons: Positively charged particles in the nucleus.

• Neutrons: Neutral particles in the nucleus.

• Electrons: Negatively charged particles in the electron cloud.

Molecules and Compounds

Formation of Molecules

Molecules are formed when two or more atoms chemically bond together. Compounds consist of atoms of different elements bonded together.

• Molecule: Two or more atoms chemically bonded (can be same or different elements).

• Compound: Two or more different types of atoms chemically bonded.

Chemical Bonding

Chemical bonds form when electrons in the valence (outermost) shell are shared or transferred between atoms.

• Valence electrons: Electrons in the outermost shell, involved in bonding.

• Octet Rule: Atoms tend to form bonds to achieve 8 electrons in their valence shell (except hydrogen, which is stable with 2).

Types of Chemical Bonds

Ionic Bonds

Ionic bonds occur when electrons are transferred from one atom to another, creating oppositely charged ions that attract each other.

• Cation: Positively charged ion (loses electrons).

• Anion: Negatively charged ion (gains electrons).

Ion Type	Charge	How Formed
Cation	Positive (+)	Loss of electrons
Anion	Negative (-)	Gain of electrons

Example: Sodium (Na) transfers an electron to Chlorine (Cl), forming Na+ and Cl-, which bond to form NaCl (table salt).

Covalent Bonds

Covalent bonds form when atoms share one or more pairs of electrons to achieve a stable electron configuration.

• Single covalent bond: Two atoms share one pair of electrons.

• Double covalent bond: Two atoms share two pairs of electrons.

Example: Two fluorine atoms share electrons to complete their octet.

Nonpolar vs. Polar Covalent Bonds

• Nonpolar covalent: Electrons shared equally; no overall charge.

• Polar covalent: Electrons shared unequally; creates charged sides (partial charges).

Example: Water (H2O) is a polar covalent molecule; electrons are pulled more towards oxygen, creating slight charges at opposite ends.

Hydrogen Bonds

Hydrogen bonds are weak attractions between the partially positive hydrogen atom of one molecule and the partially negative atom (often oxygen or nitrogen) of another molecule.

• Important in water, DNA structure, and protein folding.

• Play a role in determining the shape of complex molecules.

Solubility and Dissociation

Solubility

Solubility is the ability of one substance to dissolve in another. Water is a universal solvent in biological systems.

• Ionic and polar molecules: Dissolve in water.

• Nonpolar molecules: Do not dissolve in water (e.g., oils).

Electrolytes and Non-electrolytes

Electrolytes

Electrolytes are substances that dissociate in water to produce ions, allowing the solution to conduct electricity.

• Electrolytes: Dissociate in water; conduct electricity.

• Non-electrolytes: Do not dissociate; do not conduct electricity.

Chemical Reactions and Energy

Metabolism

Metabolism is the sum of all anabolic (building up) and catabolic (breaking down) reactions in the body.

• Anabolism: Synthesis reactions; bonds are made.

• Catabolism: Decomposition reactions; bonds are broken.

Synthesis and Decomposition Reactions

• Synthesis: Two or more reactants combine to form a larger product.

• Dehydration synthesis: Water is produced as a byproduct.

• Decomposition: Large reactant is broken down into smaller products.

• Hydrolysis: Water is split into two parts that contribute to the formation of the products.

Oxidation-Reduction (Redox) Reactions

• Oxidation: Loss of an electron by an atom.

• Reduction: Gain of an electron by an atom.

• Often coupled: one atom loses an electron (oxidized), another gains it (reduced).

Speed of Chemical Reactions

• Activation energy: Minimum energy required to start a reaction.

• Enzymes: Biological catalysts that lower activation energy, increasing reaction rates.

Heat Energy

• When chemical bonds are broken and energy is released, some is lost as heat.

Properties of Water

Mixing and Solvent Properties

• Solvent: Substance that dissolves the solute.

• Solute: Substance being dissolved.

• Solution: Uniform mixture of solvent and solute.

Solution Concentrations

• Concentration: Measure of number of particles of solute per volume of solution.

Water's Unique Properties

• Adhesion: Water sticks to other surfaces.

• Cohesion: Water sticks to itself.

• Hydrophilic: "Water-loving"; dissolves in water (ionic and polar molecules).

• Hydrophobic: "Water-fearing"; does not dissolve in water (nonpolar molecules).

Acids, Bases, and Buffers

Definitions

• Acid: Substance that releases hydrogen ions (H+).

• Base: Substance that binds to or accepts hydrogen ions.

Strength of Acids and Bases

• Strong acids/bases: Completely dissociate in water.

• Weak acids/bases: Partially dissociate in water.

The pH Scale

• Refers to hydrogen ion concentration in a solution.

• Neutral pH = 7; equal amounts of hydrogen and hydroxide ions.

Buffers

• Solutions of weak acid and weak base that resist changes in pH.

Important Ions in the Human Body

Cations	Anions
Calcium	Bicarbonate
Sodium	Phosphate
Potassium	Chloride
Hydrogen	Iodide
Iron	Ammonium
Magnesium

Organic Molecules

Carbohydrates

Carbohydrates are composed of carbon, hydrogen, and oxygen. They serve as energy sources, structural components, and are water-soluble (polar).

• Divided into monosaccharides, disaccharides, polysaccharides.

• Function: energy source, structure, elimination.

Lipids

Lipids include fats (triglycerides), phospholipids, and steroids. They are composed mostly of carbon, hydrogen, and oxygen, and are relatively insoluble in water (non-polar).

• Functions: protection, insulation, regulation, cell membranes, energy storage.

Proteins

Proteins are composed of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. They are built from amino acids and have complex structures.

• Primary structure: Sequence of amino acids.

• Secondary structure: Alpha helix or beta pleated sheet.

• Tertiary structure: Folding due to interactions with the environment.

• Quaternary structure: Interactions between multiple proteins.

• Functions: regulatory processes, transport, protection, muscle contraction, structure, energy.

Nucleic Acids

Nucleic acids are composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus. Built from nucleotides (five-carbon sugar, nitrogenous base, phosphate group).

• Types: DNA, RNA, ATP.

Oxygen and Carbon Dioxide

• Oxygen (O2): Required in the final step of cellular respiration to extract energy from food.

• Carbon dioxide (CO2): Produced during the catabolism of organic compounds.

Key Equations

• General chemical reaction: $\text{Reactants} \rightarrow \text{Products}$

• pH calculation: $\text{pH} = -\log_{10}[\text{H}^+]$

Additional info: Academic context and definitions have been expanded for clarity and completeness. Tables have been recreated and some entries inferred for completeness.