Biology Chapter 2: pH and Biological Molecules

Introduction to Biochemistry

• Biochemistry is the study of molecules that make up living organisms
• Includes carbohydrates, fats, proteins, and nucleic acids
• Important for understanding cells, basic physiology, nutrition, and health

Atoms, Ions, and Molecules

• Elements: The simplest form of matter with unique chemical properties. Identified by atomic number. Arranged in the periodic table using 1-2 letter symbols, sorted by atomic number. 91 elements occur naturally
  • 24 elements play vital roles in humans; oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus comprise 98.5% of body weight.
  • Trace elements present in small amounts but are vital. Many trace minerals are minerals, inorganics extracted from the soil by plants and passed up the food chain. Minerals are vital to body structure, enzyme function and nerve/muscle cell functions.
• Atomic Structure: Atoms composed of protons (positive charge), neutrons (no charge), and electrons (negative charge).
  • Nucleus contains protons and neutrons
  • Electrons orbit the nucleus in electron shells or energy levels. An atom electrically neutral with equal numbers of protons and electrons.
  • Valence electrons determine chemical bonding properties
• Isotopes: Varieties of an element that differ in the number of neutrons. Have similar chemical properties but different atomic masses. Atomic weight represents the average mass of all naturally occurring isotopes.
  • Radioisotopes are unstable isotopes that decay and emit radiation.
• Ions, Electrolytes, and Free Radicals: Ions are charged particles (atoms or molecules) with an uneven number of protons and electrons.
  • Anion: negatively charged ion
  • Cation: positively charged ion
  • Ionization: transfer of electrons between atoms
  • Electrolytes: substances that form ions in water; conduct electricity. Important for chemical reactivity, osmotic effects, electrical excitability of nerve and muscle.
  • Free radicals: highly reactive ions or molecules with an unpaired electron.
• Chemical Bonds: Forces that hold atoms together in molecules.

Water and Mixtures

• Water: The body's major component (50-75%). Polar covalent bonds and v-shape structure gives it unique properties essential for life:
  • Solvency: Water's ability to dissolve various substances.
  • Cohesion: Water molecules' tendency to cling to each other due to hydrogen bonds.
  • Adhesion: Water's tendency to cling to other surfaces.
  • Chemical reactivity: Water participates in various chemical reactions.
  • Thermal stability: Water's ability to resist changes in temperature.
• Mixture Types:
  • Solutions: Substances (solute) dissolved in a more abundant substance (solvent)
  • Colloids: Particles in solution are larger than in a solution; scatter light, appear cloudy.
  • Suspensions: Larger particles in solution; separate on standing.
• Acids, Bases, and pH:
  • Acids release hydrogen ions (H⁺) in water.
  • Bases accept hydrogen ions or release hydroxide ions (OH¯) in water.
  • pH is a measure of acidity; derived from the molarity of hydrogen ions (pH = -log[H†]). pH scale measures acidity and basicity. pH 7 is neutral, less than 7 is acidic and greater than 7 is basic. Maintenance of blood's normal pH is vital for physiological function.

Energy and Chemical Reactions

• Energy and Work: Energy is the capacity to do work.
  • Types of energy: potential (stored), kinetic (motion), chemical, free, heat, electromagnetic, electrical.
• Chemical Reactions: Processes where covalent or ionic bonds are formed or broken.
• Chemical Equations: Symbolic representation of chemical reactions. Shows the reactants (input), products (output), and direction of processes.
  • Classes of chemical reactions include decomposition, synthesis, and exchange reactions. Reversible reactions can proceed in either direction. Symbolized by double-headed arrow.
• Reaction Rates: Factors that affect the speed of chemical reactions, including concentration of reactants, temperature, and catalysts (enzymes are biological catalysts).
  • Catalysts lower activation energy, allowing reactions to occur rapidly at body temperature.
• Metabolism: All chemical reactions in the body. Separated into catabolism (breakdown reactions) and anabolism (synthesis reactions). Catabolism releases energy to drive anabolism.

Organic Compounds

• Carbon: Unique ability to form long chains, branched structures, and rings; readily bonds with other elements (hydrogen, oxygen, nitrogen, sulfur)
• Functional Groups: Clusters of atoms attached to the carbon backbone that determine the properties of organic molecules. Examples: hydroxyl, methyl, carboxyl, amino, phosphate.
• Monomers and Polymers: Polymers are large molecules made of repeating subunits called monomers. Dehydration synthesis and hydrolysis are crucial reactions forming and breaking polymers.
• Carbohydrates: Hydrophilic organic molecules (CH₂O)ₙ; primary source of energy. Includes monosaccharides (simple sugars like glucose, fructose, and galactose), disaccharides (double sugars like sucrose, lactose, and maltose), and polysaccharides (complex sugars like glycogen, starch, and cellulose).
• Lipids: Hydrophobic organic molecules with a high ratio of hydrogen to oxygen; rich in calories. Includes fatty acids, triglycerides, phospholipids, eicosanoids, and steroids.
  • Saturated fatty acids contain only single bonds (solids at room temperature), while unsaturated fatty acids contain one or more double or triple bonds (liquid at room temperature).
  • Trans fats are unsaturated fatty acids, where hydrogens on opposite sides of the double bond.
• Proteins: Polymers of amino acids. Amino acids have a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen and an R-group that give each amino acid its unique chemical properties. Includes primary, secondary, tertiary, and quaternary structures (important for function). 20 amino acids differ by R-group. Protein function diverse and important for structure, communication, membrane transport, catalysis, and protection among others.
• Nucleic Acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers of nucleotides. Carry and transmit genetic information