Chapter 2: The Chemical Level of Organization

Matter, Elements, and Compounds

The study of anatomy and physiology begins at the chemical level, where matter forms the basis of all living and nonliving things. Matter is anything that has mass and occupies space, and it exists in three forms: solid, liquid, and gas.

• Matter: Exists as solids (e.g., bone), liquids (e.g., blood), and gases (e.g., oxygen).

• Element: A pure substance that cannot be broken down into simpler substances by physical or chemical means.

• Compound: A substance formed from two or more elements chemically bonded together.

• Example: Water (H2O) is a compound made of hydrogen and oxygen.

Atoms and Subatomic Particles

Atoms are the smallest units of matter that retain the properties of an element. They are composed of three subatomic particles:

• Proton: Positively charged, located in the nucleus, has mass.

• Neutron: No charge, located in the nucleus, has mass.

• Electron: Negatively charged, negligible mass, orbits the nucleus in electron shells.

• Atomic Number: Number of protons in the nucleus.

• Mass Number: Number of protons plus neutrons in the nucleus.

• Electron Number: Equal to proton number in a neutral atom.

Electron Shells and Isotopes

Electrons occupy distinct energy levels called shells. Isotopes are atoms of the same element with different numbers of neutrons.

• Isotopes: Variants of an element differing in neutron number (e.g., Carbon-12, Carbon-13, Carbon-14).

• Radioisotopes: Unstable isotopes that decay over time.

Ions, Molecules, and Compounds

Ions are atoms or groups of atoms with a charge, molecules are two or more atoms bonded together, and compounds are molecules made of different elements.

• Cation: Atom that has lost electrons (positive charge).

• Anion: Atom that has gained electrons (negative charge).

• Molecule: Two or more atoms bonded (e.g., H2).

• Compound: Two or more different elements bonded (e.g., H2O).

Chemical Bonds

Chemical bonds are electrical attractions between atoms, involving the sharing, gaining, or losing of electrons in the valence shell.

• Ionic Bonds: Formed by transfer of electrons; oppositely charged ions attract (e.g., Na+ and Cl- form NaCl).

• Covalent Bonds: Formed by sharing electrons between atoms; can be single, double, or triple bonds.

• Nonpolar Covalent: Equal sharing of electrons (e.g., C-H bonds).

• Polar Covalent: Unequal sharing; one atom is more electronegative (e.g., O-H in water).

• Hydrogen Bonds: Weak attractions between a partially positive hydrogen and a partially negative atom (e.g., O or N).

Water: Structure, Properties, and Functions

Water is a polar molecule essential for life, exhibiting unique properties due to its structure and hydrogen bonding.

• Phases: Liquid, solid (ice), gas (vapor).

• Functions: Lubrication, transport, excretion, cushioning.

• Properties: Surface tension, adhesion, cohesion, high specific heat, high heat of vaporization, solvent ability.

• Polarity: Water's polarity makes it a universal solvent.

Table: Properties of Water

Water as a Universal Solvent

Water dissolves many substances due to its polarity. The ability to dissolve depends on the chemical properties of the solute.

• Hydrophilic: Polar molecules and ions dissolve in water (e.g., sugar, salt).

• Hydrophobic: Nonpolar substances do not dissolve (e.g., oil, wax).

• Amphipathic: Molecules with both polar and nonpolar regions partially dissolve (e.g., phospholipids).

• Hydration Shell: Water molecules surround dissolved ions or polar molecules.

pH and Homeostasis

pH measures the concentration of hydrogen ions (H+) in a solution, indicating its acidity or alkalinity. Maintaining pH is vital for homeostasis.

• Neutral pH: 7.0 (pure water).

• Acidic: pH < 7.0; high H+ concentration.

• Basic (Alkaline): pH > 7.0; low H+ concentration.

• Blood pH: 7.35–7.45.

pH Scale Equation:

Acids, Bases, and Buffers

Acids release H+ ions, bases release OH- ions or accept H+, and buffers resist changes in pH.

• Acid: Substance that increases H+ concentration.

• Base: Substance that increases OH- concentration or accepts H+.

• Buffer: Solution that stabilizes pH by accepting or donating H+.

• Example: Carbonic acid-bicarbonate buffer system in blood.

Buffer Reaction:

Inorganic vs. Organic Molecules

Inorganic molecules are not based on carbon and hydrogen, while organic molecules are.

• Inorganic: CO2, O2, water, acids, bases, salts.

• Organic: Carbohydrates, proteins, lipids, nucleic acids.

Chemical Reactions: Metabolism

Metabolism includes all chemical reactions in the body, divided into catabolism (decomposition) and anabolism (synthesis).

• Decomposition (Catabolism): Breaks bonds; releases energy; hydrolysis adds water.

• Synthesis (Anabolism): Forms bonds; requires energy; dehydration synthesis removes water.

Dehydration Synthesis Equation:

Hydrolysis Equation:

Carbohydrates

Carbohydrates are organic molecules with C, H, and O in a 1:2:1 ratio. They provide energy and structural support.

• Monosaccharides: Simple sugars (glucose, fructose, galactose).

• Disaccharides: Two monosaccharides joined (sucrose, maltose, lactose).

• Polysaccharides: Many monosaccharides (glycogen, starch, cellulose).

• Example: Glycogen is the storage form of glucose in animals.

Lipids

Lipids are hydrophobic organic molecules, including fats, oils, and steroids. They store energy, insulate, and protect.

• Fatty Acids: Saturated (straight, no double bonds), unsaturated (kinked, one or more double bonds), polyunsaturated (multiple double bonds).

• Triglycerides: Glycerol + 3 fatty acids; main energy storage lipid.

• Phospholipids: Two fatty acids, glycerol, phosphate group; major component of cell membranes.

• Steroids: Ring-shaped lipids (e.g., cholesterol, sex hormones).

• Prostaglandins: Derived from unsaturated fatty acids; involved in signaling.

Table: Types of Lipids

Nucleic Acids

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

• DNA: Double-stranded helix; stores genetic information; bases: adenine, guanine, cytosine, thymine.

• RNA: Single-stranded; involved in protein synthesis; bases: adenine, guanine, cytosine, uracil.

• Nucleotide: Composed of a pentose sugar, phosphate group, and nitrogenous base.

• Purines: Adenine, guanine.

• Pyrimidines: Cytosine, thymine, uracil.

Table: DNA vs. RNA

Adenosine Triphosphate (ATP)

ATP is the energy currency of the cell, produced by catabolic reactions and used in anabolic reactions.

• Catabolic Reaction: ATP breaks down to ADP + P + energy.

• Anabolic Reaction: ADP + P + energy forms ATP.

ATP Hydrolysis Equation:

ATP Synthesis Equation:

Proteins

Proteins are polymers of amino acids, essential for structure and function in the body.

• Amino Acids: 20 types; some are essential (must be consumed).

• Peptide Bond: Joins amino acids via dehydration synthesis.

• Protein Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha-helix or beta-pleated sheet (hydrogen bonds).

  • Tertiary: Further folding and bonding.

  • Quaternary: Multiple polypeptide chains (e.g., hemoglobin).

• Function: Determined by shape; shape determined by amino acid sequence.

• Denaturation: Loss of shape and function due to changes in temperature or pH.

Enzymes

Enzymes are protein catalysts that lower activation energy, speeding up chemical reactions in cells.

• Activation Energy: Minimum energy required to start a reaction.

• Specificity: Each enzyme catalyzes one reaction; reusable; optimal pH and temperature.

• Enzyme-Substrate Complex: Substrates bind to active site, reaction occurs, products released.

Enzyme Reaction Steps:

1. Substrates approach active site.

2. Substrates bind, forming enzyme-substrate complex.

3. Reaction occurs, products formed.

4. Products released, enzyme reused.