AP Biology Biochemistry Notes

AP Biology Biochemistry Notes

Chemistry Basics
  • Atoms: Smallest unit of an element that maintains chemical properties.
Subatomic Particles
  • Protons: Positive charge, located in nucleus, defines atomic number.
  • Neutrons: Neutral charge, similar in size to protons, number varies in isotopes.
  • Electrons: Negative charge, located in the electron cloud, number can change (ions).
Molecules
  • Molecule: Two or more atoms covalently bonded.
  • Electron Levels (E levels/e- shells): Locations of electrons; energy changes affect their distance from nucleus.
  • Valence Shell: Outermost shell where valence electrons reside.
  • Valence Electrons: Important for chemical properties; atoms typically need 8 for stability (octet).
Chemical Bonds
1. Covalent Bonds
  • Formed by sharing valence electrons.
  • Molecules can be polar (electrical charge) or non-polar.
  • Electronegativity: Atom's tendency to attract electrons; varies (H < O & N).
2. Ionic Bonds
  • Occur between metals and non-metals (transfer of electrons).
  • Form salts, which dissolve in water, creating cations and anions.
3. Hydrogen Bonds
  • Weak attractions between polar molecules; significant in water.
4. Van der Waals Interactions
  • Temporary attractions due to electron position changes in atoms.
Properties of Water for Biology
  • High Specific Heat: Maintains stable temperatures, excellent for homeostasis.
  • Universal Solvent: Dissolves ions and polar molecules, aiding transport in organisms.
  • High Heat of Vaporization: Evaporative cooling (sweat, transpiration).
  • Cohesion and Adhesion: Important for water transport in plants.
  • Expansion upon Freezing: Ice floats, insulating water below, supporting aquatic life.
Organic Chemistry
  • Organic Compounds: Primarily carbon-based, crucial for life.
  • Miller/Urey Experiment: Demonstrated organic molecules can form from inorganic compounds.
Macromolecules and Polymers
  • Polymers: Large molecules made of monomers linked by covalent bonds.
  • Dehydration Synthesis: Process to form polymers, releasing water.
  • Hydrolysis: Process to break down polymers using water.
Categories of Organic Macromolecules
1. Carbohydrates
  • Types: Monosaccharides (simple sugars), Polysaccharides (complex sugars).
  • Function: Energy source and structural components.
    • Examples: Glucose, Fructose, Starch (energy storage in plants), Glycogen (energy storage in animals), Cellulose (structural support in plants).
2. Lipids
  • Characteristics: Mostly non-polar, hydrophobic; includes fats, oils, steroids.
  • Types: Triglycerides, Phospholipids (important for cell membranes), Steroids (hormonal functions).
  • Structure Determinants: Saturated vs. Unsaturated fats, Trans fats impact on health.
3. Proteins
  • Structure: Composed of amino acids linked by peptide bonds.
  • Levels of Structure:
    1. Primary: Sequence of amino acids.
    2. Secondary: Folding patterns (alpha helix, beta sheet).
    3. Tertiary: Overall 3D shape of a polypeptide.
    4. Quaternary: Arrangement of multiple polypeptides.
  • Denaturation: Loss of structure due to factors like pH, temperature, which affects function.
Nucleic Acids
  • Function: Store and transfer genetic information (DNA, RNA).
  • Structure: Nucleotides with a pentose sugar, phosphate group, and nitrogenous base.
    • DNA: Double-stranded, deoxyribose, codes for proteins.
    • RNA: Single-stranded, ribose, involved in protein synthesis (mRNA, tRNA, rRNA).
Biogeochemical Cycles
1. Nitrogen Cycle
  • Conversion of atmospheric nitrogen into usable forms via nitrogen-fixing bacteria and nitrifying bacteria.
  • Processes: Nitrogen fixation, Nitrification, Denitrification, Ammonification.
2. Phosphorus Cycle
  • Phosphorus found in rocks, released into soil/water, incorporated into organic compounds by plants.
  • Decomposers recycle phosphorus back into the soil.
Summary
  • Understanding the basic structures and functions of atoms, molecules, and macromolecules is crucial in AP Biology, particularly biochemistry and how they relate to life processes and cycles.