Chemistry Foundations for Anatomy & Physiology: Atoms, Bonds, and Macromolecules

Chapter 2 – Chemistry Foundations for Anatomy & Physiology

Major Parts of an Atom & Its Structure

Atoms are the fundamental units of matter, composed of three primary subatomic particles:

• Protons: Positively charged particles located in the nucleus.

• Neutrons: Neutral particles also found in the nucleus.

• Electrons: Negatively charged particles that orbit the nucleus in electron shells.

The nucleus contains protons and neutrons, while electrons move in defined energy levels around the nucleus. The number of protons defines the atomic number and the element's identity.

The Periodic Table

The periodic table organizes all known elements by increasing atomic number. Elements in the same column (group) have similar chemical properties due to the same number of valence electrons. Rows (periods) indicate increasing energy levels.

• Groups: Vertical columns; elements share chemical properties.

• Periods: Horizontal rows; elements have the same number of electron shells.

The periodic table is essential for predicting element behavior in biological systems.

Oxidation Numbers

Oxidation numbers (or states) indicate the degree of oxidation (loss of electrons) of an atom in a chemical compound. They are used to track electron transfer in redox reactions.

• For example, in water (H2O), hydrogen has an oxidation number of +1, and oxygen is -2.

Key Chemical Terms and Definitions

• Isotope: Atoms of the same element with different numbers of neutrons, resulting in different mass numbers.

• Ionic bond: A chemical bond formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

• Ion: An atom or molecule with a net electric charge due to the loss or gain of electrons.

• Anion: A negatively charged ion (gains electrons).

• Cation: A positively charged ion (loses electrons).

• Covalent bond: A chemical bond formed when two atoms share one or more pairs of electrons.

• Nonpolar molecule: A molecule in which electrons are shared equally, resulting in no significant charge separation.

• Hydrogen bond: A weak bond between a hydrogen atom (covalently bonded to an electronegative atom) and another electronegative atom (often oxygen or nitrogen).

Solutions and Chemical Reactions

• Solvent: The substance in which a solute is dissolved to form a solution (e.g., water in biological systems).

• Solute: The substance dissolved in a solvent.

• Dehydration synthesis (condensation): A chemical reaction in which two molecules are joined by removing a water molecule. This process forms polymers from monomers.

• Hydrolysis: A chemical reaction that breaks bonds between two molecules by the addition of water; the reverse of dehydration synthesis.

• Exergonic reaction: A chemical reaction that releases energy (often in the form of heat).

• Endergonic reaction: A chemical reaction that requires an input of energy.

• Salts: Ionic compounds that dissociate in water to form ions other than H+ or OH-.

• Acids: Substances that release hydrogen ions (H+) in solution; proton donors.

• Bases: Substances that accept hydrogen ions or release hydroxide ions (OH-); proton acceptors.

• pH: A measure of hydrogen ion concentration; $pH = -\log[H^+]$

• Neutralization: A reaction between an acid and a base to produce a salt and water.

Macromolecules: Structure and Function

There are four major classes of biological macromolecules essential for life: carbohydrates, proteins, nucleic acids, and lipids.

Carbohydrates

• Monomers: Monosaccharides (simple sugars, e.g., glucose)

• Structure: Consist of carbon, hydrogen, and oxygen in a 1:2:1 ratio (CnH2nOn).

• Function: Provide energy (e.g., glucose), energy storage (e.g., starch in plants, glycogen in animals), and structural support (e.g., cellulose in plant cell walls).

Proteins

• Monomers: Amino acids (20 standard types)

• Structure:

  • Primary: Sequence of amino acids

  • Secondary: Alpha helices and beta sheets formed by hydrogen bonding

  • Tertiary: 3D folding due to side chain interactions

  • Quaternary: Association of multiple polypeptide chains

• Functions: Enzymes, structural support, transport, signaling, immune response, etc.

• Key terms: Denaturation (loss of structure/function), enzyme (biological catalyst), substrate (reactant for enzyme), active site (enzyme region binding substrate), coenzyme (organic cofactor).

Nucleic Acids

• Monomers: Nucleotides (composed of a sugar, phosphate group, and nitrogenous base)

• Structure: DNA (double helix), RNA (single strand)

• Function: Store and transmit genetic information (DNA, RNA), direct protein synthesis.

Lipids

• Monomer structure: Lipids do not have a true monomer, but are composed of fatty acids and glycerol in various arrangements.

• Types of Lipids:

  1. Triglycerides: Composed of glycerol and three fatty acids; function as energy storage. Fatty acids can be saturated (no double bonds) or unsaturated (one or more double bonds).

  2. Phospholipids: Composed of glycerol, two fatty acids, and a phosphate group; major component of cell membranes.

  3. Steroids: Four fused carbon rings; function as hormones (e.g., cholesterol, testosterone).

Macromolecule	Monomer	Structure	Main Functions
Carbohydrate	Monosaccharide	Ring or linear chains of C, H, O	Energy, storage, structure
Protein	Amino acid	Polypeptide chains, 4 levels of structure	Enzymes, structure, transport, signaling
Nucleic Acid	Nucleotide	Phosphate-sugar-base units	Genetic information, protein synthesis
Lipid	None (fatty acids, glycerol)	Triglycerides, phospholipids, steroids	Energy storage, membranes, hormones

Example: Starch (a carbohydrate) is a polymer of glucose monomers and serves as energy storage in plants. Hemoglobin (a protein) is composed of four polypeptide chains and transports oxygen in blood.

Additional info: This foundational chemistry content is essential for understanding the molecular basis of anatomy and physiology, including cell structure, metabolism, and biochemical reactions.