AP Biology Exam Review: Biochemistry

Bonds: Ionic, Covalent, Hydrogen

  • Ionic Bonds: Strong bonds formed through the transfer of electrons between atoms.
  • Covalent Bonds:
    • Polar: Unequal sharing of electrons, creating partial charges.
    • Nonpolar: Equal sharing of electrons.
  • Hydrogen Bonds: Weak bonds between partially positive hydrogen and partially negative atoms.
  • Relative Strengths: Understanding the relative strengths of each bond type.
  • Bond Usage in Nature: Knowing where each bond type is utilized in biological systems.

Molecules and Atoms from the Environment

  • Essential Elements: C, H, N, O, P, and S are crucial for building new molecules in living organisms.
  • Carbon (C):
    • Found: In all four macromolecules (carbohydrates, lipids, proteins, nucleic acids).
    • Carbon Cycle: Understand its cycling between environment and living organisms.
  • Nitrogen (N):
    • Found: In proteins and nucleic acids.
    • Nitrogen Cycle: Understand its cycling between environment and living organisms.
  • Phosphorus (P):
    • Found: In lipids and nucleic acids.
    • Phosphorus Cycle: Understand its cycling between environment and living organisms.
  • Usage in Macromolecules: Know where and how C, H, N, O, P, and S are used in macromolecules.

Properties of Water

  • Origin: All properties stem from water’s polarity and ability to form hydrogen bonds.
  • Excellent Solvent:
    • Dissolving Capability: Water dissolves polar and ionic compounds due to its polarity.
    • Cellular Fluids: Water-based cellular fluids facilitate biological processes.
  • Cohesion and Adhesion:
    • Transpiration: Cohesion and adhesion aid in water transport in plants.
  • Density as a Solid:
    • Ice Formation: Water is less dense as a solid, preventing ponds and lakes from freezing solid.
  • High Heat Capacity/Specific Heat:
    • Evaporative Cooling: Sweating in animals moderates body temperature.
    • Temperature Moderation: Large bodies of water moderate air temperatures.

pH: Acid-Base Scale

  • Scale: 0-14, determined by the number of H+H^+ ions.
  • Logarithmic Scale: pH 3 = 10−310^{-3} = 11000\frac{1}{1000} concentration of H+H^+ ions.
  • Examples:
    • Blood: 7.4
    • Stomach: 2
    • Small Intestine: 8
  • Enzyme Specificity: Enzymes are specific to pH levels.

Reactions of Life

  • Dehydration Synthesis:
    • Process: Releases water to create polymers connected by covalent bonds.
    • Nature: Anabolic and endergonic (requires energy).
  • Hydrolysis:
    • Process: Uses water to break polymers into monomers by breaking covalent bonds.
    • Nature: Catabolic and exergonic (releases energy).

Macromolecules

  • Carbohydrates
    • Ratio: CHO in 1:2:1 ratio
    • Monomers: Monosaccharides (know basic structure and examples)
    • Dimers: Disaccharides (know basic structure, formation, and examples)
    • Polymers: Polysaccharides (know basic structure, formation, and examples like cellulose, starch, chitin, and glycogen)
  • Lipids
    • Elements: C, H, O (not a 1:2:1 ratio; P only in phospholipids)
    • Basic Structure: Fatty acid chains and a polar region
    • Saturation: Degree of saturation affects structure (unsaturated = kinks, liquid at room temperature; saturated = straight, solid at room temperature)
    • Phospholipids: Form cell membranes (double layer), amphipathic (hydrophilic and hydrophobic)
    • Functions: Cell membrane (phospholipids), energy storage (fats, oils), steroid hormones (cholesterol variations), insulation, myelin sheath.
  • Proteins
    • Elements: C, H, O, N (may have S in R group)
    • Monomers: Amino acids (20 different R groups determine properties)
    • Amino Acid Structure: Carboxyl group (COOH), amino group (NH2), central carbon, variable R group
    • Protein Folding: Shape determines function
      • Primary Structure: Amino acid chain
      • Secondary Structure: Beta pleated sheet or alpha helix (hydrogen bonds between non-adjacent carboxyl and amino groups)
      • Tertiary Structure: Globular; folds in on itself (disulfide bridges, hydrogen bonds, hydrophobic interactions; ionic bonding between R groups)
      • Quaternary Structure: More than one polypeptide
    • Functions: Enzymes (amylase), structure (keratin), transport (hemoglobin), signaling (oxytocin), protein carriers, antibodies
  • Nucleic Acids
    • Elements: C, H, O, N, and P
    • Monomers: Nucleotides (nitrogenous bases, phosphate groups, deoxyribose sugars)
    • Polymers: DNA and RNA
    • Nucleotide Composition: Sugar, phosphate, and base
    • DNA: Double-stranded, deoxyribose, A, G, C, T
    • RNA: Single-stranded, ribose, A, G, C, U
      • mRNA: Copies genetic message
      • rRNA: Attaches mRNA and makes up ribosomes
      • tRNA: Carries amino acids
    • Function: Storage and transmission of genetic information

Enzymes

  • Biological Catalysts: Proteins that speed up reactions by lowering activation energy
  • Active Site: Region where reaction occurs (exposed R groups)
  • Enzyme Action: Break down (catabolic) or build up (anabolic) substances
  • Enzyme/Substrate Complex: Forms during reaction
  • Substrate: What the enzyme acts on
  • Rate Factors: Determined by collisions between substrate and enzyme
  • Nomenclature: Ends in -ase, often named after substrate
  • Specificity: Enzyme is specific to substrate
  • Enzyme Rate Factors:
    • pH: Optimal for each enzyme
    • Temperature: Increased temperature initially increases rate, excessive heat can denature enzyme
    • Enzyme Concentration: More enzyme = faster rate
    • Substrate Concentration: More substrate = faster rate, until saturation
  • Endergonic vs. Exergonic: Understand and analyze reaction curves; explain energy coupling
  • Inhibition:
    • Competitive Inhibition: Competes for active site; overcome with more substrate
    • Non-competitive Inhibition: Attaches at allosteric site, changes enzyme shape; cannot be overcome with more substrate
  • Coenzymes & Cofactors: Coenzymes (organic) and cofactors (inorganic) interact with enzymes to enable function.