Detailed Notes on Molecular Bonding and Water Properties

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  • Case Study on Friday!
  • Syllabus Quiz due Jan 17th at 11:59 PM
  • Quiz 1: Opens on Friday and closes Monday; covers slides from the 1st day of class, and subsequent days (W, F, M, W, F).
    • Format: Multiple choice, to be taken with lockdown browser and monitor.
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Molecular Bonding Section (M2 L2)

Electronegativity
  • Definition:
    • The tendency of an atom (e.g., oxygen) in a molecule to attract shared electrons towards itself.
  • Analogy:
    • Electronegativity = Greediness
    • Greedy atoms do not share electrons fairly.
Determining Bond Polarity
  1. Find the difference in electronegativity.
  2. Take the absolute value.
  3. Interpret the value:
    • 0.40 - 2.00 Pauling units: Bond is POLAR
    • Less than 0.40 Pauling units: Bond is NONPOLAR
Common Elements and Electronegativity
  • Activity: Rank the order of the four most common elements in living organisms by electronegativity.
    • Important for memorization!
Polarity Relevant Concepts
  • Polarity depends on both bond types and molecular shape.
  • Importance of Polarity:
    • Determines molecular shape and interaction patterns.
    • Creates a separation of electric charge across compounds, resulting in a negatively charged end and positively charged end.
Types of Bonds
Non-Polar Covalent Bonds
  • Equal sharing of electrons.
    • Example: Methane (CH4)
    • Carbon equally shares electrons with four hydrogen atoms.
Polar and Non-Polar Solvents
  • Solubility Rules:
    • Like dissolves like:
      • Polar solvents dissolve polar solutes (e.g., NaCl in water).
      • Non-polar solvents dissolve non-polar solutes (e.g., oil).
Biological Importance of Molecular Structures
  • Atoms build molecules (which build cells):
    • Proteins: Composed of amino acids.
    • Carbohydrates: Composed of sugars (e.g., glucose).
    • Lipids: Composed of glycerol and fatty acids.
    • Nucleic Acids: Comprised of nucleotides.
Amino Acids & Protein Structure
  • Amino acids have various side chains (R-groups) that determine protein function.
Influence of Polarity on Molecular Interactions
  • R-groups of amino acids lead to various non-covalent bonds (e.g., hydrogen and ionic).
  • Polar residues are typically on the outside of protein molecules.
Ionic Bonds Overview
  • Ionic bonds form when metals lose electrons, and non-metals gain electrons to fulfill the octet rule.
    • Salt Formation: Produced by reactions between acids and bases; involves transfer of electrons.
Bond Types
  • Ionic Bonds: Transfer of electrons from metals to non-metals.
  • Covalent Bonds: Sharing of electron pairs between atoms.
  • Hydrogen Bonds: Attraction between hydrogen and electronegative atoms (O, F, N).
Intermolecular Forces
  • Types of attractive forces between molecules:
    1. Van der Waals Forces: Weakest.
    2. Dipole-Dipole Interactions: Moderate strength.
    3. Hydrogen Bonds: Stronger interactions (between δ+ of hydrogen and δ- of electronegative atom).
Importance of Hydrogen Bonds
  • Hydrogen Bonds:
    • Weak forces that form and break frequently (important in molecular interactions).
    • Example: Behavior in ice vs. liquid water.
Water's Unique Properties Due to Hydrogen Bonds
  • Cohesion: Water molecules stick to themselves, allowing for surface tension.
  • Adhesion: Water molecules can stick to other substances.
  • Allows for capillary action in plants.
Water and Climate Regulation
  • Water’s high specific heat:
    • Can absorb/release a large amount of heat with minimal temperature change
    • Specific heat of liquid water is 4.179 J/(kg·K).
Importance of pH in Biological Systems
  • Definitions:
    • Acidic solution: pH < 7, [H+] > [OH-]
    • Basic solution: pH > 7, [OH-] > [H+]
  • Buffers: Substances that maintain pH within a narrow range necessary for life.
    • Example: Blood buffer system, based on carbonic acid.
Summary of Water's Role
  • Water is essential for:
    • Life processes: Respiration, DNA replication, digestion, etc.
    • Environmental stability: High heat of vaporization helps moderate temperatures.