Module 1: The Chemistry of Life - Elements, Bonds & Water

Essential Elements of Life

• To understand how living things work, we can focus on just four key elements:

  • Hydrogen (H)

  • Carbon (C)

  • Nitrogen (N)

  • Oxygen (O)

• These four elements collectively constitute approximately 96\% of all living things.

• Water is also an essential molecule discussed, mediating many biochemical reactions in cells and covering a significant portion of our planet.

• Understanding these basic chemistry principles, especially concerning water, is crucial for comprehending fascinating biomolecules like proteins, carbohydrates, lipids, and nucleic acids (e.g., DNA and RNA) that form cells.

Chemical Elements and Atoms

• Elements: Distinctive types of matter, with approximately 118 unique substances identified to date (e.g., Helium (He), Chlorine, Sulfur).

• Atoms: The smallest fundamental units of elements.

  • Each atom has a unique structure defined by a distinct number of protons, which determines its identity.

  • Nucleus: At the center of the atom, containing:

    • Protons: Positively charged (+1). Their number defines the element.

    • Neutrons: Electrically neutral (0).

  • Electron Shells: Areas around the atomic exterior where negatively charged electrons move.

    • Electrons: Negatively charged (-1).

  • Typically, atoms have an equal number of protons and electrons, rendering them electrically neutral.

• Ions: Atoms that have either gained or lost electrons, resulting in a net positive or negative charge.

Chemical Bonds

• Molecules: Structures made of two or more atoms connected by chemical bonds. They are more complex than simple atoms.

• Ionic Bonds: Formed when oppositely charged ions are attracted to each other (e.g., Sodium Chloride (NaCl) which involves Na^+ and Cl^- ions).

• Covalent Bonds: Formed by two atoms sharing electrons.

  • Electron Pairs: Electrons in the outer shells of atoms prefer to exist in pairs, which contributes to increased atomic stability.

  • Example: Molecular hydrogen (H_2) is more stable than a single hydrogen atom because its electrons are paired.

  • Hydrogen Atom: A very small atom, typically consisting of just one proton and one electron, with no neutrons.

  • Hydrogen Ion (H^+): Lacks its electron, simplifying it to just a proton.

Polarity in Covalent Bonds

• Nonpolar Covalent Bond: Occurs when two atoms forming a covalent bond share electrons equally. This happens when the atoms have similar electronegativity (e.g., in H_2).

• Polar Covalent Bond: Occurs when electrons are not shared equally between atoms, particularly common in biomolecules.

Electronegativity

• Definition: The phenomenon where some atoms hold electrons more closely to the positive charges in their nuclei than other atoms do.

• Visualization: Periodic tables often illustrate electronegativity, with highly electronegative atoms (e.g., Oxygen) often shown in red and less electronegative atoms in yellow.

• Biological Relevance: The four major biological elements exhibit varying electronegativities:

  • Oxygen (O) is more electronegative than Nitrogen (N).

  • Nitrogen (N) is more electronegative than Carbon (C).

  • Carbon (C) has approximately the same electronegativity as Hydrogen (H).

• Partial Charges: Differences in electronegativity create partial negative (\delta^-) and partial positive (\delta^+) charges on atoms within a molecule. These partial charges play crucial roles in the structure and function of complex biomolecules like DNA and proteins.

Hydrogen Bonds

• Definition: An attraction between a partial positive charge (\delta^+) on a hydrogen atom of one molecule and a partial negative charge (\delta^-) on an atom (most commonly oxygen or nitrogen due to their high prevalence in living organisms) in a different molecule.

• Notation: Represented by dashed lines (e.g., ---) to distinguish them from stronger covalent bonds, which are shown with solid lines.

• Strength: Hydrogen bonds are generally not as strong as covalent bonds.

• Biological Importance: Super important for biological processes, such as holding the two strands of DNA together in the double helix structure.

The Peculiar Properties of Water

• Centrality to Life: Water is incredibly central to life. For example, humans can survive about a month without food but usually only a few days without water.

  • All cellular biochemistry occurs in water.

  • Water makes up over half of your body mass.

• Unique Properties: Water possesses properties that are unique among molecules.

• Interactions with Water: The ability to predict which molecules or regions of a molecule can interact with water is a vital skill in biology.

  • Hydrophilic Molecules: Can interact with water because they possess partial charges required for forming hydrogen bonds (e.g., Glucose, which can form multiple hydrogen bonds with water).

  • Hydrophobic Molecules: Cannot interact with water because they lack the necessary partial charges (e.g., molecules with many carbon-hydrogen bonds, where electrons are shared equally due to similar electronegativities, thus lacking partial charges).

Acids, Bases, and pH

• Water's Dual Role: Water molecules can act as both an acid and a base:

  • They can pick up a proton (H^+) to form hydronium ions (H_3O^+).

  • They can drop a proton (H^+) to form hydroxide ions (OH^-).

• Acid: An ion or molecule that releases a proton (H^+).

• Base: An ion or molecule that acquires a proton (H^+).

• pH: A measure of the concentration of protons (H^+) in a solution. It operates on a logarithmic scale.

  • Acids: Have a high concentration of protons.

  • Bases: Have a low concentration of protons.

  • Neutral Water: Has a pH that is halfway between strong acids and strong bases.

• Significance: The concentration of protons (pH) is crucial for many biological processes.

Applications of Water's Properties

• Sweating: Water's properties (specifically its high heat capacity and heat of vaporization) are vital for cooling the body through sweating.

• Climate Moderation: These principles can be applied to understand phenomena such as the moderate climates found in coastal cities (due to the high heat capacity of large bodies of water).

• Climate Change: Understanding water's properties is also key to comprehending how oceans respond to global climate change.