2 - Aqueous chemistry

Lecture Information

  • Course: BIOC 2300 - Lecture 2

  • Topic: Aqueous Chemistry

  • Instructor: David N. Langelaan

  • Location: Room 8F, Tupper Medical Building

  • Contact Email: dlangela@dal.ca

  • Content Questions Contact: BIOC2300@dal.ca

Session Objectives

  • Review fundamental concepts

  • Describe non-covalent interactions, their strengths, and implications for biological interactions

  • Explain water molecule's electronic arrangement and properties

  • Explain the hydrophobic effect and its influence on biomolecular structures and assembly

Main Classes of Biomolecules

  • Nucleic Acids: Composed of nucleotides

  • Proteins: Composed of amino acids

  • Carbohydrates: Composed of monosaccharides

  • Lipids: Diverse, energy-rich molecules

  • Commonality: All essential for life

Elements of Biochemistry

  • Composition: 92% of human dry weight is made up of CHNOPS (Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur)

  • Role of Elements: Form covalent bonds

  • Common Ions: K+, Mg++, Na+, Ca++, Cl-

  • Stability of Elements: Small size contributes to stability and non-radioactivity

Electronegativity

  • Definition: Ability of an element to attract shared electrons

  • Implications: Determines ionic vs. covalent bonding

  • Selected Elements:

    • Fluorine (F): 4.0

    • Oxygen (O): 3.5

    • Nitrogen (N): 3.0

    • Carbon (C): 2.5

    • Hydrogen (H): 2.1

Lewis Dot Symbols

  • Bonds: Atoms engage in

    • Covalent Bonds: Sharing of electrons

    • Ionic Bonds: Transfer of electrons

  • Valence Shell: Completed by either 2 or 8 electrons

Oxidation Numbers

  • Definition: Charge an atom would have if all bonds were ionic

  • Example Assessment: Oxidation state of carbon in glucose-6-phosphate

Geometry of Molecules

  • Influence on Polarity: Number of bonded atoms and electron pairs influences molecular shape and polarity

Non-Polar Molecules Assessment

  • Understanding which molecules are non-polar (e.g., CO2) based on electronegativity differences.

Amphipathic Molecules

  • Definition: Contain both polar and non-polar functional groups

  • Types: Hydrophilic, hydrophobic, amphipathic

Summary of Non-Covalent Interactions

  • Types:

    • Van der Waals

    • Hydrogen bonds

    • Ionic interactions

  • Cohesion and Adhesion: Fundamental in biological specificity and molecular interactions

Water as a Critical Molecule

  • **Properties: **

    • Very polar, bent structure

    • Forms hydrogen bonds

    • High melting, boiling points, and surface tension due to strong H-bonds

Hydrophobic Effect

  • Definition: Non-polar substances aggregate in water

  • Thermodynamic Explanation: Related to entropy changes of water molecules in contact with non-polar substances

Protein Folding and Compartmentalization

  • Consequences of Hydrophobic Effect:

    • Formation of lipid bilayers and compartments in cells

Key Concepts to Understand

  • Terms:

    • Entropy, Enthalpy

    • Electronegativity

    • Covalent Bonds, Non-Covalent Bonds

    • Polar/Non-Polar definitions, Amphipathic

    • Water structure, Hydrophobic Effect

  • References for Further Reading:

    • P&C chapters 1 and 2

    • Lehninger and other biochemistry texts