Fundamental Chemistry Concepts for Anatomy & Physiology

Module 2.1 Atoms and Elements

Matter and Chemistry

Matter is anything that occupies space and has mass. Chemistry is the study of matter and the changes it undergoes, which is foundational for understanding biological processes in Anatomy & Physiology.

• Matter: Exists in solid, liquid, and gas forms.

• Chemistry: Explains the composition, structure, and changes of matter.

Atoms and Atomic Structure

Atoms are the smallest units of matter that retain the properties of an element. Their structure determines chemical behavior.

• Atom: Consists of a nucleus (protons and neutrons) and electrons orbiting the nucleus.

• Subatomic particles:

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

  • Neutrons (n0): Neutral particles in the nucleus.

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

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

  • The number of neutrons can vary, resulting in isotopes.

• Electron shells:

  • The first shell holds up to two electrons.

  • The second shell holds up to eight electrons.

Elements in the Periodic Table and the Human Body

Elements are pure substances consisting of only one type of atom. The human body is composed of major, minor, and trace elements.

• Atomic number: Number of protons in an atom, determines the element.

• Major elements: Hydrogen, oxygen, carbon, nitrogen.

• Minor elements: Seven elements present in smaller amounts.

• Trace elements: Thirteen elements present in very small amounts.

Isotopes and Radioactivity

Isotopes are atoms of the same element with different numbers of neutrons. Some isotopes are radioactive and can be used in medical imaging.

• Mass number: Sum of protons and neutrons.

• Isotope: Atoms with the same number of protons but different numbers of neutrons.

• Radioisotopes: Unstable isotopes that emit radiation.

Module 2.2 Matter Combined: Mixtures and Chemical Bonds

Mixtures

Mixtures are combinations of two or more substances physically intermixed without changing their chemical nature.

• Suspensions: Large particles that settle out over time.

• Colloids: Intermediate-sized particles that do not settle.

• Solutions: Homogeneous mixtures with very small particles.

  • Solute: Substance dissolved.

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

Chemical Bonds

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

• Molecule: Two or more atoms bonded together.

• Compound: Molecule containing two or more different elements.

• Inert: Atoms with full electron shells, chemically unreactive.

Ions and Ionic Bonds

Ionic bonds form when electrons are transferred from one atom to another, creating charged particles called ions.

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

• Opposite charges attract, forming ionic compounds (salts).

Covalent Bonds

Covalent bonds involve the sharing of electrons between atoms.

• Nonpolar covalent bonds: Equal sharing of electrons.

• Polar covalent bonds: Unequal sharing, resulting in partial charges.

• Polar molecules: Molecules with regions of partial charge.

• Hydrogen bonds: Weak attractions between partially positive hydrogen and partially negative atoms (e.g., oxygen). Responsible for water's surface tension.

Module 2.3 Chemical Reactions

Chemical Notation and Equations

Chemical notation uses symbols and abbreviations to represent chemical reactions. The basic form is the chemical equation.

• Reactants: Substances entering a reaction.

• Products: Substances produced by a reaction.

Types of Chemical Reactions

• Reversible reactions: Can proceed in both directions.

• Catabolic reactions: Decomposition reactions that break down molecules.

• Anabolic reactions: Synthesis reactions that build molecules.

• Exchange reactions: Atoms are exchanged between molecules.

• Oxidation-reduction (redox) reactions: Electrons are transferred; oxidation is loss, reduction is gain.

Energy and Chemical Reactions

Energy is required for chemical reactions and exists in several forms in the body.

• Potential energy: Stored energy.

• Kinetic energy: Energy of motion.

• Chemical energy: Stored in chemical bonds.

• Electrical energy: Movement of charged particles.

• Mechanical energy: Directly involved in moving matter.

• Endergonic reactions: Require energy input.

• Exergonic reactions: Release energy.

Reaction Rates and Enzymes

Enzymes are biological catalysts that speed up reactions by lowering activation energy.

• Activation energy ($E_a$): Minimum energy required for a reaction.

• Factors increasing reaction rate:

  • Reactant concentration

  • Temperature

  • Physical state (solid, liquid, gas)

• Enzymes are not consumed in reactions and can be denatured by extreme conditions.

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

Inorganic Compounds

Inorganic compounds do not contain both carbon and hydrogen. Water, acids, bases, and salts are essential for physiological processes.

Water

Water is the most abundant inorganic compound in the body and has several vital properties.

• High heat capacity: Absorbs and releases heat slowly.

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

• Cushions and protects: Surrounds and protects organs.

• Lubricant: Reduces friction between surfaces.

• Universal solvent: Dissolves many substances.

• Polar covalent molecule: Unequal sharing of electrons creates polarity.

• Hydrophilic: Water-loving substances dissolve easily.

• Hydrophobic: Water-fearing substances do not dissolve easily.

Acids and Bases

Acids and bases are substances that release hydrogen ions (H+) or hydroxide ions (OH-) in solution, respectively.

• Acid: Releases H+ ions.

• Base: Releases OH- ions.

• pH scale: Measures acidity or alkalinity (0–14).

  • Neutral: pH = 7

  • Acidic: pH < 7

  • Basic (alkaline): pH > 7

  • Blood pH: 7.35–7.45; inside cells pH ≈ 7.2

• Buffer: Stabilizes pH by absorbing or releasing H+ ions.

Module 2.5 Organic Compounds: Carbohydrates, Lipids, Proteins, and Nucleic Acids

Monomers and Polymers

Organic compounds are built from monomers (single units) that join to form polymers (large molecules).

• Dehydration synthesis: Builds polymers by removing water.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

Carbohydrates are the body's main source of energy and are classified by size.

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

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

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

Lipids

Lipids are hydrophobic molecules important for energy storage, insulation, and cell membranes.

• Fatty acids:

  • Saturated fatty acids: No double bonds.

  • Monounsaturated fatty acids: One double bond.

  • Polyunsaturated fatty acids: Multiple double bonds.

• Triglycerides: Neutral fats, main energy storage.

• Phospholipids: Major component of cell membranes.

• Steroids: Include hormones and cholesterol.

Proteins

Proteins are polymers of amino acids and perform a wide range of functions in the body.

• Amino acids: Building blocks of proteins.

• Peptide bonds: Link amino acids together.

• Protein structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha helix and beta-pleated sheet.

  • Tertiary: 3D folding of the polypeptide.

  • Quaternary: Multiple polypeptides joined.

Nucleotides and Nucleic Acids

Nucleic acids store and transmit genetic information. They are composed of nucleotides.

• Nucleotide structure: Phosphate group, sugar, nitrogenous base.

• Nitrogenous bases:

  • Purines: Double-ringed (adenine (A), guanine (G)).

  • Pyrimidines: Single-ringed (cytosine (C), uracil (U), thymine (T)).

• Adenosine triphosphate (ATP): Main energy carrier in cells.

• Deoxyribonucleic acid (DNA):

  • Contains adenine, guanine, cytosine, thymine.

  • Double helix structure; strands held by hydrogen bonds.

  • Base pairing: A–T (two hydrogen bonds), C–G (three hydrogen bonds).

  • Encodes genetic information for protein synthesis.

• Ribonucleic acid (RNA):

  • Contains adenine, guanine, cytosine, uracil.

  • Single-stranded; uracil replaces thymine (A–U pairing).

  • Contains pentose sugar ribose.

Comparison Table: Types of Chemical Bonds

Bond Type	Mechanism	Example	Strength
Ionic	Transfer of electrons	NaCl (table salt)	Moderate
Covalent	Sharing of electrons	H2O (water)	Strong
Hydrogen	Attraction between polar molecules	Between water molecules	Weak

Key Equations

• Activation Energy: $E_a$

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

Additional info: Academic context and definitions have been expanded for clarity and completeness.