SC

The Chemical Level of Organization

The Chemical Level of Organization Study Notes

2.1 Elements and Atoms

  • Key Definitions

    • Matter: Anything that has mass and takes up space.
    • Mass: Amount of matter in an object.
    • Weight differs from mass as it depends on gravity.
    • Different from Atomic Mass.
    • Element: Pure substance made of only one type of atom.
    • Atom: Smallest unit of an element that retains its properties.

  • Subatomic Particles:

    • Protons: Positive charge, found in the nucleus.
    • Neutrons: Neutral charge, found in the nucleus.
    • Electrons: Negative charge, orbit the nucleus in shells/clouds.

  • Atomic Properties:

    • Atomic Number = number of protons.
    • Atomic Mass = protons + neutrons.
    • Isotopes: Same element, different neutron numbers (e.g., Carbon-12, Carbon-13, Carbon-14).
    • Radioactive Isotopes: Unstable; used in medicine (e.g., PET scans, cancer treatment).

Compounds & Molecules

  • Compound: Substance with 2 or more different elements chemically bonded (e.g., H₂O, NaCl).
  • Molecule: Two or more atoms bonded (can be same element, e.g., O₂).
  • Example: Glucose (C₆H₁₂O₆) contains carbon, hydrogen, and oxygen.

Radiology

  • Radiology: Use of radiation in medical imaging and treatment.
  • Medical Use of Isotopes:
    • Pros: Diagnostic imaging (PET), targeted therapy (radiation therapy).
    • Cons: Radiation damage, requires strict training & regulation.

2.2 Chemical Bonds

  • Valence Electrons: Outer-shell electrons that determine reactivity.
  • Bonds formed by electron interactions (transfer or sharing).

Types of Bonds:

  1. Ionic Bond (electron transfer)

    • Atoms become ions (charged).
      • Cations (+): lost electrons (e.g., K⁺, Mg²⁺).
      • Anions (-): gained electrons (e.g., Cl⁻).
    • Example: NaCl.

  2. Covalent Bond (electron sharing)

    • Strongest bond.
    • Can be:
      • Polar (unequal sharing; e.g., water).
      • Nonpolar (equal sharing; e.g., O₂, CH₄).
    • Water is polar → hydrogen bonding between molecules.

  3. Hydrogen Bond (weak attraction between polar molecules)

    • Important in DNA base pairing, protein folding, and water cohesion.
    • Example: Found in a glass of water (covalent bonds in H₂O, hydrogen bonds between molecules).
  • Electronegativity trend: Increases left → right across the periodic table; influences bond polarity.

2.3 Chemical Reactions

  • Types of Energy:

    • Kinetic: Energy of motion.
    • Potential: Stored energy.
    • Chemical: Energy stored in bonds (e.g., ATP).
    • Mechanical: Movement of objects (muscles).
    • Radiant: Light energy.
    • Electrical: Flow of charged particles (nerves).

  • Chemical Reactions: Reactants → Products

    1. Synthesis (Anabolic): A + B → AB
    2. Decomposition (Catabolic): AB → A + B
    3. Exchange: AB + CD → AD + CB
    4. Reversible: Can proceed both directions (A + B ⇌ AB).

  • Factors Affecting Reaction Rates:

    • Reactant properties (surface area, particle size).
    • Temperature (↑ temp = ↑ rate).
    • Concentration/Pressure (↑ concentration = ↑ collisions).
    • Catalysts/Enzymes (lower activation energy).

2.4 Inorganic Compounds Essential to Life

  • Water Properties:
    • Universal solvent (hydrophilic substances dissolve).
    • Hydrophobic molecules repel water (e.g., lipids).
    • Hydrolysis Reaction: Break polymers with water.
    • Dehydration Synthesis: Build polymers by removing water.

Solutions & Concentration

  • Solution = Solvent + Solute.
  • Molarity (M) = Moles of solute per liter.
  • Colloid: Medium particles that do not settle (e.g., milk).
  • Suspension: Large particles that settle over time (e.g., blood).

Salts

  • Formed by ionic bonds.
  • Dissociate in water into ions → electrolytes (e.g., Na⁺, Cl⁻, K⁺).

pH Scale

  • Acid: Releases H⁺ (pH < 7).
  • Base: Accepts H⁺ (pH > 7).
  • Neutral: pH = 7 (pure water).
  • Human Blood: ~7.35–7.45 (slightly basic).
  • Buffers: Stabilize pH (e.g., bicarbonate buffer system).
  • Examples:
    • Stomach acid ~ pH 1–2 (very acidic).
    • HCl in water → fully dissociates (strong acid).
    • H₃PO₄ in water → partially dissociates (weak acid).

2.5 Organic Compounds Essential to Life

  • General Features:
    • Always contain carbon & hydrogen.
    • Carbon forms 4 covalent bonds → allows diverse molecules.

Functional Groups (important for biochemistry)

  • Hydroxyl (–OH): Polar, found in carbohydrates.
  • Carboxyl (–COOH): Found in amino and fatty acids.
  • Amino (–NH₂): Found in proteins.
  • Methyl (–CH₃): Modifies activity of molecules.
  • Phosphate (–PO₄²⁻): Found in ATP, nucleic acids.

Four Major Organic Compounds:

  1. Carbohydrates:

    • General formula: C₆H₁₂O₆ (1C:2H:1O).
    • Monosaccharides: glucose, fructose.
    • Disaccharides: maltose, sucrose.
    • Polysaccharides: starch, glycogen, cellulose.
    • Stored as glycogen in humans.
    • Main fuel source (ATP production).

  2. Lipids:

    • Nonpolar, hydrophobic.
    • Types:
      • Triglycerides: glycerol + 3 fatty acids (energy storage).
      • Saturated: solid at room temp (animal fat).
      • Unsaturated: liquid at room temp (plant oils).
      • Trans fats: artificially hydrogenated, harmful.
      • Phospholipids: Amphipathic (polar head + nonpolar tail); make up cell membranes.
      • Steroids: 4-ring structure (cholesterol, hormones).

  3. Proteins:

    • Monomers: Amino acids (20 types).
    • Bonds: Peptide bonds (covalent).
    • Structure:
      • Primary: Amino acid sequence.
      • Secondary: α-helix, β-sheet (H-bonds).
      • Tertiary: 3D folding of one.
      • Quaternary: Multiple polypeptides.
    • Functions: Enzymes, structure, transport, defense.
    • Enzymes: Speed up reactions, not consumed.

  4. Nucleic Acids:

    • DNA: Double helix, deoxyribose sugar, bases (A, T, C, G).
    • RNA: Single-stranded, ribose sugar, bases (A, U, C, G).
      • Types: mRNA, tRNA, rRNA.
    • ATP: Modified nucleotide; energy carrier.
      • Phosphorylation: Adding a phosphate group.

Chapter 2 Big Picture Summary

  • Atoms form bonds → molecules → life’s chemistry.
  • Water is essential for life due to polarity & hydrogen bonding.
  • pH homeostasis is critical for human survival.
  • Organic molecules (carbs, lipids, proteins, nucleic acids) are the building blocks of cells.

Sample Exam Questions

  1. Compare and contrast ionic and covalent bonds with examples.
  2. Why are hydrogen bonds important in DNA and protein structure?
  3. Explain why water is considered the universal solvent.
  4. What is the difference between a strong acid (HCl) and a weak acid (H₃PO₄)?
  5. A patient’s blood pH is 6.8. Explain what is happening and how the body responds.
  6. Describe the four levels of protein structure with an example of each.
  7. Why are phospholipids critical for cell membranes?