The Chemical Level of Organization

The Chemical Level of Organization: Chapter 2

Atoms, Molecules, and Bonds

  • Atoms: Smallest, most stable units of matter.
    • Protons (+-charge) and Neutrons (no charge) are in the nucleus.
    • Electrons ( --charge) are in an orbital 'cloud' outside the nucleus.
  • Atomic Number: Number of protons.
  • Atomic Mass: Number of protons and neutrons.
  • Number of protons usually equals the number of electrons.
  • Elements: Classification of atoms based on their atomic number.

Electrons and Reactivity

  • Electron Shells/Energy Levels: Electrons are organized into shells$.
  • Outermost shell electrons have the most energy.
  • Valence Shell: Number of electrons in the outermost shell determines an atom's reactivity.
    • 1^{st} shell: up to 2 electrons.
    • 2^{nd} and 3^{rd} shells: up to 8 electrons.
  • Unstable (reactive) atoms tend to bond to form molecules.

Chemical Bonds

  • Hold atoms together to form molecules and compounds.
  • Covalent Bonds: Atoms share electrons to fill outermost shells.
    • Nonpolar: Electrons shared equally (e.g., O_2).
    • Polar: Electrons shared unequally due to differing attraction (e.g., H_2O).
  • Ionic Bonds: Electrons are transferred between atoms, forming charged ions.
    • Cation: Positively charged atom (lost electrons).
    • Anion: Negatively charged atom (gained electrons).
    • Form between cations and anions due to electrostatic attraction (e.g., NaCl).
  • Hydrogen Bonds: Weak bonds between a hydrogen atom and an oxygen or nitrogen atom (intermolecular, e.g., H_2O, DNA, proteins).

Chemical Notation

  • H = one atom of hydrogen.
  • 2H = two atoms of hydrogen, not bonded.
  • H_2 = two hydrogen atoms bonded to make a hydrogen molecule.
  • H_2O = one molecule with two hydrogen atoms and one oxygen atom bonded.
  • Ions:
    • Na^+ = sodium atom lost one electron.
    • Cl^- = chlorine atom gained one electron.
    • Ca^{2+} = calcium atom lost two electrons.

Chemical Reactions

  • Decomposition (Catabolic): AB \to A + B (releases energy).
  • Synthesis (Anabolic): A + B \to AB (requires energy).
  • Exchange: AB + CD \to AC + BD.
  • Metabolism: Total of all chemical reactions in the body.
  • Reversible Reactions: All reactions are theoretically reversible (A + B \rightleftharpoons AB).
  • Equilibrium: Forward and reverse reaction rates are balanced.

Enzymes, Energy, and Chemical Reactions

  • Enzymes: Special proteins that speed up (catalyze) chemical reactions by lowering activation energy.
  • Substrates: Molecules that interact with an enzyme.
  • Active Sites: Specific sites on an enzyme where substrates bind.
  • Specificity: Each enzyme has uniquely shaped active sites.
  • Enzymes are reusable.
  • Optimal Function: Each enzyme has optimal temperature (37 ^{\circ}C or 98 ^{\circ}F) and pH (usually neutral, pH 7).
  • Denaturation: High temperatures destroy active sites, causing loss of function.

Water: Special Properties

  • Solubility: Many polar substances (e.g., glucose, ammonia) dissolve in water.
  • Reactivity: Participates in chemical reactions (e.g., hydrolysis, dehydration synthesis).
  • High Heat Capacity: Absorbs and retains heat, aiding temperature regulation.
  • Lubrication: Reduces friction between surfaces (e.g., joints).

Water Molecules & Solutions

  • Electrolytes: Soluble inorganic molecules (e.g., NaCl) that dissociate into charged ions in water.
    • Aqueous solutions with ions conduct electrical charges (essential for muscle, nerve, heart functions).
  • Polar Molecules: Dissolve in water but do not dissociate into ions.

pH of Body Fluids

  • pH: Measures hydrogen ion (H^+) concentration.
    • <7.0 = acid (H^+ increase).
    • >7.0 = base/alkaline (H^+ decrease, OH^- increase).
    • 7.0 = neutral.
  • Acids: Solutes releasing H^+ in water (e.g., HCl).
  • Bases: Solutes releasing OH^- in water; OH^- combines with H^+ to form H_2O (e.g., NaOH).
  • Buffers: Compounds resisting pH changes.
    • Carbonic acid-bicarbonate buffer system (CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons HCO_3^- + H^+) maintains blood pH (7.35-7.45).

Organic Compounds

  • Contain carbon (C), hydrogen (H), and usually oxygen (O).
  • Monomers: Simple forms of organic compounds.
  • Polymers: Complex forms of organic compounds.
  • Dehydration Synthesis: Builds polymers by removing a water molecule (H_2O).
  • Hydrolysis: Breaks down polymers by adding a water molecule (H_2O).

Four Principal Types of Organic Compounds

  1. Carbohydrates (Sugars):
    • Important energy source.
    • Contain C:H:O in a near 1:2:1 ratio.
    • Monomer: Monosaccharide (e.g., glucose, C6H{12}O_6).
    • Polymer: Polysaccharide (e.g., starch in plants, glycogen in animals).
  2. Lipids (Fats, Oils, Waxes):
    • Insoluble in water.
    • Components of cell membranes, important energy reserves.
    • Classes: Fatty acids, triglycerides, phospholipids, glycolipids, steroid lipids.
      • Fatty Acids (Monomer): Long carbon chains with a carboxyl group (COOH) (hydrophilic end) and a hydrocarbon tail (hydrophobic end).
        • Saturated: Maximum hydrogen atoms.
        • Unsaturated: Some carbons lack maximum hydrogen atoms.
      • Triglycerides (Polymer): Glycerol + three fatty acids.
      • Phospholipids & Glycolipids: Components of cell membranes with hydrophilic heads and hydrophobic tails.
      • Steroid Lipids: Large molecules with a complex four-ring structure (e.g., cholesterol for structure, testosterone/estrogen as hormones).
  3. Proteins:
    • Six principal types: Structural, Contractile, Transport, Enzymes, Buffering, Antibodies.
    • Monomer: Amino acids (20 types).
      • Joined by Peptide bonds (covalent) to form peptides/polypeptides.
      • Chains longer than 100 amino acids are proteins.
    • Protein Structure: Primary (linear chain), Secondary (alpha-helix, pleated sheet), Tertiary (3D folding), Quaternary (multiple polypeptide chains).
  4. Nucleic Acids (DNA, RNA):
    • Store and process molecular-level information in cells.
    • Monomer: Nucleotides.
      • Composed of: Phosphate group, Pentose sugar (ribose in RNA, deoxyribose in DNA), Nitrogenous base (Adenine A, Guanine G, Cytosine C, Thymine T in DNA, Uracil U in RNA).
    • DNA: Double-stranded, helical (A-T, G-C pairing).
    • RNA: Single-stranded.

Adenosine Triphosphate (ATP)

  • High-energy compound.
  • ATP-ADP Cycle: Hydrolysis of ATP to ADP releases energy for cellular functions (e.g., muscle contraction, nerve impulses).