Basic Chemistry

Introduction to Matter

Chemistry is foundational to understanding Anatomy & Physiology, as all living and nonliving things are composed of matter and energy. Matter and energy interact to form the basis of all biological processes.

• Matter: Anything that has mass and occupies space. It can be seen, smelled, and/or felt.

• Weight: Mass plus the effects of gravity.

• States of Matter:

  • Solid: Definite shape and volume.

  • Liquid: Changeable shape; definite volume.

  • Gas: Changeable shape and volume.

Energy

Energy is essential for all physiological processes, as it enables work and movement within the body.

• Energy: The capacity to do work or put matter into motion. It does not have mass or occupy space.

• The greater the work done, the more energy is used up.

• Forms of Energy:

  • Kinetic Energy: Energy in action (e.g., muscle contraction).

  • Potential Energy: Stored (inactive) energy (e.g., energy stored in chemical bonds).

• Energy can be transformed from potential to kinetic energy.

Types of Energy in the Body

• Chemical Energy: Stored in bonds of chemical substances (e.g., ATP).

• Electrical Energy: Results from movement of charged particles (e.g., nerve impulses).

• Mechanical Energy: Directly involved in moving matter (e.g., muscle movement).

• Radiant/Electromagnetic Energy: Travels in waves (e.g., heat, visible light, ultraviolet light, X-rays).

Energy Conversion: Energy may be converted from one form to another, but some energy is always lost as heat, making the process inefficient.

Atoms and Elements

Elements

All matter is composed of elements, which are substances that cannot be broken down into simpler substances by ordinary chemical means.

• Four elements make up 96% of the human body: Carbon (C), Oxygen (O), Hydrogen (H), and Nitrogen (N).

• The periodic table lists all known elements.

Atoms

• Atoms: The smallest particles of an element that retain the properties of that element.

• Atomic Symbol: One- or two-letter chemical shorthand for each element (e.g., O for oxygen, Na for sodium).

• Atoms are composed of three subatomic particles:

  • Protons: Positively charged, found in the nucleus.

  • Neutrons: No charge, found in the nucleus.

  • Electrons: Negatively charged, orbit around the nucleus.

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

Atomic Number and Mass Number

• Atomic Number: Number of protons in the nucleus; written as a subscript to the left of the atomic symbol (e.g., 3Li).

• Mass Number: Total number of protons and neutrons; written as a superscript to the left of the atomic symbol (e.g., 7Li).

Isotopes

• Isotopes are structural variations of the same element with the same number of protons but different numbers of neutrons (different mass numbers).

Combining Matter

Molecules and Compounds

• Molecule: General term for two or more atoms bonded together (e.g., O2).

• Compound: Specific molecule that has two or more different kinds of atoms bonded together (e.g., H2O).

Mixtures

Most matter exists as mixtures, which are physical combinations of two or more components.

• Solutions: Homogeneous mixtures; particles are evenly distributed. Solvent: Substance present in greatest amount (usually water). Solute: Substance dissolved in solvent (e.g., glucose in blood plasma).

• Colloids (Emulsions): Heterogeneous mixtures; particles are not evenly distributed and do not settle out (e.g., cytosol).

• Suspensions: Heterogeneous mixtures with large, visible solutes that settle out (e.g., blood cells in plasma).

Chemical Bonds

Electron Shells and Chemical Bonds

• Electrons occupy regions called electron shells (energy levels) around the nucleus.

• Each shell can hold a specific number of electrons: Shell 1 (2 electrons), Shell 2 (8 electrons), etc.

• The valence shell is the outermost electron shell; electrons here have the most potential energy and are involved in chemical reactions.

• Octet Rule: Atoms tend to gain, lose, or share electrons to have 8 electrons in their valence shell (except H and He, which want 2).

Types of Chemical Bonds

• Ionic Bonds: Involve the transfer of valence electrons from one atom to another, resulting in ions (cations and anions) that are attracted by opposite charges.

• Covalent Bonds: Involve the sharing of electrons between atoms. - Single bond: Sharing 2 electrons. - Double bond: Sharing 4 electrons. - Triple bond: Sharing 6 electrons.

• Nonpolar Covalent Bonds: Electrons are shared equally, resulting in electrically balanced molecules (e.g., CO2).

• Polar Covalent Bonds: Electrons are shared unequally, creating molecules with partial charges (e.g., H2O). - The atom with greater electron-attracting ability is electronegative; the other is electropositive. - Such molecules are called dipoles.

• Hydrogen Bonds: Weak attractions between a hydrogen atom (already covalently bonded to another atom) and an electronegative atom. Important in water and in stabilizing large molecules (e.g., proteins, DNA).

Chemical Reactions

Types of Chemical Reactions

• Synthesis (Combination) Reactions: Atoms or molecules combine to form a larger, more complex molecule. Used in anabolic (building) processes.

• Decomposition Reactions: Breakdown of a molecule into smaller molecules or atoms. Used in catabolic (bond-breaking) processes.

• Exchange (Displacement) Reactions: Involve both synthesis and decomposition; bonds are made and broken.

Energy Flow in Chemical Reactions

• Exergonic Reactions: Net release of energy; products have less potential energy than reactants.

• Endergonic Reactions: Net absorption of energy; products have more potential energy than reactants.

Factors Affecting Reaction Rates

• Temperature (higher temperature increases rate)

• Concentration of reactants (higher concentration increases rate)

• Particle size (smaller particles increase rate)

• Catalysts (increase rate without being consumed; enzymes are biological catalysts)

Biochemistry

Inorganic Compounds

Water

• Makes up 60–80% of cell volume; most abundant and important inorganic compound in the body.

• Key properties:

  • High Heat Capacity: Absorbs and releases heat with little temperature change.

  • High Heat of Vaporization: Evaporation requires large amounts of heat (important for cooling).

  • Polar Solvent Properties: Dissolves and dissociates ionic substances; forms hydration layers around large molecules; major transport medium.

  • Reactivity: Necessary for hydrolysis and dehydration synthesis reactions.

  • Cushioning: Protects organs from physical trauma (e.g., cerebrospinal fluid).

Salts

• Dissociate in water into cations (positive) and anions (negative).

• All ions are called electrolytes because they conduct electrical currents in solution.

• Ions such as sodium, potassium, calcium, and iron play specialized roles in body functions.

• Ionic balance is vital for homeostasis.

Acids and Bases

• Acids: Proton donors; release H+ in solution (e.g., HCl → H+ + Cl–).

• Bases: Proton acceptors; release OH– in solution (e.g., NaOH → Na+ + OH–).

pH: Acid-Base Concentration

• pH measures the concentration of hydrogen ions [H+] in a solution.

• Acidic solutions: High [H+], low pH (0–6.99).

• Neutral solutions: Equal H+ and OH– ions; pH 7 (pure water).

• Alkaline (basic) solutions: Low [H+], high pH (7.01–14).

Organic Compounds

• Contain carbon (except CO2 and CO, which are inorganic).

• Major types: carbohydrates, lipids, proteins, nucleic acids.

• Many are polymers made of repeating monomers.

• Synthesized by dehydration synthesis; broken down by hydrolysis.

Carbohydrates

• Include sugars and starches; contain C, H, O (H:O ratio is 2:1).

• Three classes:

  • Monosaccharides: Simple sugars (3–7 carbons); general formula .

  • Disaccharides: Double sugars; formed by dehydration synthesis of two monosaccharides (e.g., sucrose, maltose, lactose).

  • Polysaccharides: Polymers of monosaccharides; storage forms (e.g., starch in plants, glycogen in animals).

Lipids

• Contain C, H, O (less O than carbohydrates), sometimes P; insoluble in water.

• Main types:

  • Triglycerides (Fats and Oils): Three fatty acids bonded to a glycerol molecule; used for energy storage, insulation, and protection.

    • Saturated fatty acids: Single bonds; solid at room temperature (e.g., animal fats).

    • Unsaturated fatty acids: One or more double bonds; liquid at room temperature (e.g., plant oils).

    • Trans fats: Modified oils; unhealthy.

    • Omega-3 fatty acids: "Heart healthy" fats.

  • Phospholipids: Modified triglycerides; glycerol, two fatty acids, and a phosphorus group. Head is hydrophilic, tails are hydrophobic; important in cell membranes.

  • Steroids: Four interlocking ring structures; cholesterol is the most important steroid (building block for vitamin D, steroid hormones, bile salts, and cell membranes).

Proteins

• Comprise 20–30% of cell mass; most varied functions (structural, enzymes, contraction).

• Contain C, H, O, N, sometimes S and P.

• Polymers of amino acids joined by peptide bonds.

• Four structural levels:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha helices (coils) and beta sheets (ribbons).

  • Tertiary: How secondary structures interact.

  • Quaternary: How two or more polypeptides interact.

• Shapes:

  • Fibrous proteins: Strandlike, water-insoluble, stable (e.g., collagen, keratin).

  • Globular proteins: Compact, spherical, water-soluble, sensitive to environment (e.g., enzymes, antibodies).

• Denaturation: Loss of 3-D shape and function due to environmental changes (e.g., temperature, pH).

• Enzymes: Globular proteins that act as biological catalysts; lower activation energy and increase reaction speed.

Enzyme Action

• Enzymes are specific for their substrates; names often end in -ase (e.g., hydrolase, oxidase).

• Three steps in enzyme action:

  1. Substrate binds to enzyme's active site.

  2. Enzyme-substrate complex undergoes internal rearrangements.

  3. Product is released; enzyme is free to catalyze another reaction.

Nucleic Acids

• Composed of C, H, O, N, P; largest molecules in the body.

• Polymers of nucleotides (monomers).

• Two major classes:

  • DNA (Deoxyribonucleic Acid): Double helix in the nucleus; genetic blueprint for protein synthesis. Nucleotides contain deoxyribose, phosphate, and one of four nitrogen bases (A, G, C, T). Base pairing: A–T, G–C.

  • RNA (Ribonucleic Acid): Single-stranded; active outside nucleus; contains ribose and uracil (instead of thymine). Three types: mRNA, tRNA, rRNA.

ATP (Adenosine Triphosphate)

• Energy currency of the cell; chemical energy released from glucose breakdown is captured in ATP.

• Structure: Adenine-containing RNA nucleotide with two additional phosphate groups.

• ATP directly powers chemical reactions in cells, providing immediate, usable energy.