Atoms, Elements, Chemical Bonds, and Water: Foundations for Anatomy & Physiology

Module 2.1: Atoms and Elements

Definition of Matter

In anatomy and physiology, matter refers to anything that has mass and occupies space. Matter exists in three states: solid, liquid, or gas. Chemistry is the study of matter and its interactions, which is foundational for understanding physiological processes.

Atoms and Atomic Structure

• Atom: The smallest unit of matter that retains its chemical properties. Atoms are composed of subatomic particles: protons, neutrons, and electrons.

• Subatomic Particles:

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

  • Neutrons (n): Neutral charge, also found in the nucleus.

  • Electrons (e-): Negatively charged, found outside the nucleus in electron shells.

• Atoms are electrically neutral when the number of protons equals the number of electrons.

• The atomic nucleus contains protons and neutrons.

Electron Shells

• Electrons occupy regions called electron shells around the nucleus.

• Shells have specific capacities:

  • First shell: up to 2 electrons

  • Second shell: up to 8 electrons

  • Third shell: up to 18 electrons (often "satisfied" with 8)

Elements and the Periodic Table

• An element is a substance that cannot be broken down by chemical means.

• Each element is defined by its atomic number (number of protons).

• The periodic table organizes elements by properties and atomic number.

• The human body is primarily composed of hydrogen, oxygen, carbon, and nitrogen, plus minerals and trace elements.

Isotopes and Radioactivity

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

• Isotopes: Atoms of the same element with different numbers of neutrons.

• Radioisotopes: Unstable isotopes that emit radiation as they decay, used in medical imaging and treatments.

Module 2.2: Matter Combined: Mixtures and Chemical Bonds

Mixtures

A mixture is a physical combination of two or more substances without chemical bonding.

• Suspensions: Large particles that settle out (e.g., blood cells in plasma).

• Colloids: Medium-sized particles that do not settle (e.g., cytosol).

• Solutions: Small, evenly distributed particles that do not settle (e.g., salt in water).

  • Solute: Substance dissolved.

  • Solvent: Substance doing the dissolving (often water).

Chemical Bonds

Chemical bonds are attractive forces that hold atoms together in molecules and compounds.

• Molecule: Two or more atoms bonded together.

• Compound: Molecule composed of atoms from different elements.

• Macromolecules: Large molecules made of many atoms (e.g., proteins, DNA).

Valence Electrons and the Octet Rule

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

• Octet rule: Atoms are most stable with eight electrons in their valence shell.

Ions and Ionic Bonds

• Ions: Charged atoms formed by gaining or losing electrons.

  • Cation: Positively charged ion (loss of electrons).

  • Anion: Negatively charged ion (gain of electrons).

• Ionic bond: Attraction between oppositely charged ions, forming compounds called salts.

Covalent Bonds

• Formed when atoms share electron pairs.

• Single, double, or triple bonds depending on number of shared pairs.

• Electronegativity: Tendency of an atom to attract electrons; increases from bottom left to top right of the periodic table.

Nonpolar and Polar Covalent Bonds

• Nonpolar covalent bonds: Electrons shared equally (e.g., O2).

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

Hydrogen Bonds and Surface Tension

• Hydrogen bonds: Weak attractions between partially positive hydrogen and partially negative atoms (e.g., oxygen).

• Surface tension: Water molecules are attracted to each other, creating a "skin" on the surface.

Module 2.3: Chemical Reactions

Chemical Notation

• Reactants: Starting substances in a chemical reaction.

• Products: Substances formed by the reaction.

• Reversible reactions: Indicated by double arrows ($A + B \rightleftharpoons AB$).

Energy in Chemical Reactions

• Energy: Capacity to do work.

  • Potential energy: Stored energy.

  • Kinetic energy: Energy of motion.

• Chemical energy: Stored in chemical bonds.

• Electrical energy: Movement of charged particles.

Types of Chemical Reactions

• Catabolic (decomposition) reactions: Break down molecules ($AB \rightarrow A + B$).

• Anabolic (synthesis) reactions: Build larger molecules ($A + B \rightarrow AB$).

• Exchange reactions: Swap components ($AB + CD \rightarrow AD + BC$).

• Oxidation-reduction (redox) reactions: Transfer electrons between atoms.

Reaction Rates and Enzymes

• Reaction rates depend on concentration, temperature, particle size, and catalysts.

• Enzymes: Biological catalysts that lower activation energy and speed up reactions.

• Substrate: The molecule an enzyme acts upon.

• Enzymes are specific and not consumed in reactions.

Module 2.4: Inorganic Compounds: Water, Acids, Bases, and Salts

Water

• Water is vital for life, with properties such as high heat capacity, cushioning, and acting as a solvent.

• Water is a polar molecule, allowing it to dissolve ionic and polar covalent substances.

• Hydrophilic: Substances that dissolve in water.

• Hydrophobic: Substances that do not dissolve in water.

Acids and Bases

• Acids: Proton donors; increase hydrogen ion ($H^+$) concentration.

• Bases: Proton acceptors; decrease hydrogen ion concentration, often by releasing hydroxide ions ($OH^-$).

• The strength of an acid or base is measured by its effect on $[H^+]$ in solution.

Inorganic vs. Organic Compounds

• Inorganic compounds: Do not contain both carbon and hydrogen (e.g., water, salts).

• Organic compounds: Contain both carbon and hydrogen (e.g., carbohydrates, proteins, lipids, nucleic acids).

Table: Comparison of Mixture Types

Type	Particle Size	Settling	Example
Suspension	Large	Settles out	Blood cells in plasma
Colloid	Medium	Does not settle	Cytosol
Solution	Small	Does not settle	Salt in water

Table: Types of Chemical Reactions

Type	General Formula	Description
Catabolic (Decomposition)	$AB \rightarrow A + B$	Breaks down molecules
Anabolic (Synthesis)	$A + B \rightarrow AB$	Builds larger molecules
Exchange	$AB + CD \rightarrow AD + BC$	Swaps components
Redox (Oxidation-Reduction)	Electron transfer	Transfers electrons between atoms

Additional info:

• Some context and examples have been expanded for clarity and completeness.

• Scientific terms have been defined and explained for self-contained study.