Chemistry Foundations for Anatomy & Physiology: Matter, Atoms, and Biological Macromolecules

Chemistry and Its Role in Anatomy & Physiology

What is Chemistry?

Chemistry is the physical science that studies the properties of matter and the changes it undergoes. Understanding chemistry is essential for grasping the chemical level of organization in the human body, which underpins all physiological processes.

• Matter: Anything that takes up space and has mass.

• Three states of matter: Solids, Liquids, and Gases.

Principle Elements of the Body

The human body is composed of several key elements, including carbon, hydrogen, oxygen, and nitrogen, which are fundamental to biological molecules and physiological processes.

The Atom

Structure of the Atom

An atom is the smallest unit of matter, composed of subatomic particles:

• Protons (p+): Positively charged particles found in the nucleus.

• Neutrons (n): Electrically neutral particles also located in the nucleus.

• Electrons (e-): Negatively charged particles orbiting the nucleus in electron shells.

The nucleus contains protons and neutrons, while electrons are found in the electron cloud surrounding the nucleus.

Atomic Number & Atomic Mass

• Atomic Number: Number of protons in the nucleus (also equals the number of electrons in a neutral atom).

• Atomic Mass: Total number of protons and neutrons in the nucleus.

Electron Shells and Valence Electrons

• Electrons occupy energy levels called electron shells.

• 1st shell: Maximum 2 electrons; 2nd and 3rd shells: Maximum 8 electrons each.

• Valence electrons: Electrons in the outermost shell, crucial for chemical reactivity.

Atoms, Ions, and Chemical Bonds

Inert and Reactive Elements

• Inert elements: Have filled outer electron shells and do not react (e.g., noble gases).

• Reactive elements: Have unfilled valence shells and tend to gain, lose, or share electrons to achieve stability.

Ions: Cations and Anions

• Cations: Atoms that have lost electrons, resulting in a positive charge (e.g., Na+).

• Anions: Atoms that have gained electrons, resulting in a negative charge (e.g., Cl-).

Chemical Bonds

• Covalent Bonds: Atoms share electrons.

  • Non-polar covalent bonds: Electrons shared equally (e.g., O2, H2).

  • Polar covalent bonds: Electrons shared unequally, creating partial charges (e.g., H2O).

• Ionic Bonds: Formed by the electrical attraction between cations and anions (e.g., NaCl).

• Hydrogen Bonds: Weak attractions between the positive charge on hydrogen (in a polar molecule) and a negative charge on another atom (e.g., between water molecules).

Water and Its Biological Importance

Properties of Water

• Exists in all three states of matter (solid, liquid, gas).

• Essential for all bodily functions.

• Hydrogen bonding gives water unique properties such as high surface tension and solvent capabilities.

Water as a Universal Solvent

• Solution: A mixture of solute (dissolved substance) and solvent (dissolving agent).

• Water dissolves many substances due to its polarity, facilitating ionization and dissociation of molecules.

• Hydrophilic molecules dissolve readily in water; hydrophobic molecules do not.

Electrolytes

• Electrolytes: Inorganic substances whose ions conduct electrical currents in solution, essential for muscle and nerve function.

pH Scale and Homeostasis

• The pH scale measures hydrogen ion concentration; it is logarithmic (a change of 1 pH unit = 10-fold change in [H+]).

• Normal blood plasma pH: 7.35–7.45.

• Acidosis: pH below 7.35; can depress the central nervous system.

• Alkalosis: pH above 7.45; can cause uncontrollable muscle contractions.

Macromolecules in Physiology

Organic vs. Inorganic Compounds

• Organic compounds: Contain large amounts of carbon and hydrogen (e.g., sugars, fats, proteins).

• Inorganic compounds: Generally lack large amounts of carbon and hydrogen (e.g., water, salts, CO2).

Macromolecules: Structure and Function

• Macromolecules: Large molecules made of repeating subunits called monomers.

• Polymers: Chains of monomers formed by dehydration synthesis (removal of water to form bonds).

• Hydrolysis: Breaking polymers into monomers by adding water.

Lipids

• Triglycerides: Glycerol + 3 fatty acids; energy storage, insulation, and protection.

• Fatty acids: Hydrophilic head (carboxyl group) and hydrophobic tail (hydrocarbon chain).

• Saturated fatty acids: No double bonds; solid at room temperature.

• Unsaturated fatty acids: One or more double bonds; liquid at room temperature.

• Eicosanoids: Lipid signaling molecules (e.g., inflammation).

• Steroids: Involved in hormone synthesis.

• Phospholipids: Main component of cell membranes.

Carbohydrates

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

• Disaccharides: Two monosaccharides linked together.

• Polysaccharides: Long chains of monosaccharides (e.g., glycogen).

• Glycogen: Storage form of glucose in liver and muscle.

Nucleic Acids

• Nucleic acids: Long chains of nucleotides; DNA stores genetic information, RNA is involved in protein synthesis.

• Nucleotide structure: Nitrogenous base (purines: A, G; pyrimidines: C, T, U), 5-carbon sugar, phosphate group.

Proteins

• Proteins: Polymers of amino acids; diverse functions including enzymes, signaling, and structure.

• Structure determines function: Primary, secondary, tertiary, and quaternary structures.

Protein-Ligand Interactions

Binding Properties

• Specificity: Ability of a protein to bind a particular ligand.

• Affinity: Strength of attraction between protein and ligand.

• Saturation: Fraction of binding sites occupied by ligand.

• Competition: Multiple ligands compete for the same binding site; antagonists inhibit binding.

Protein Modulation

• Allosteric modulation: Modulators bind at regulatory sites, altering protein activity (activators increase, inhibitors decrease activity).

• Physical modulators: pH, temperature, and salt concentration can denature proteins, affecting function.

• Up-regulation: Increases protein synthesis.

• Down-regulation: Decreases protein synthesis.

Representative Molecular Structures

The following image illustrates the molecular structures of common substances relevant to physiology, such as propane (fuel), acetic acid (vinegar), and acetylsalicylic acid (aspirin). These examples highlight the diversity of organic molecules and their importance in biological and medical contexts.