Chemistry for Biology: Atoms and Molecules Study Notes

Atoms

Introduction to Atoms and Molecules

  • Chapter 2: Chemistry for Biology

Definitions

  • Atoms: The fundamental building blocks of matter, composed of subatomic particles (protons, neutrons, and electrons).

  • Molecules: Chemical structures consisting of two or more atoms bonded together.

Atomic Model: Example of Helium

  • Atomic Model: Visualization of an atom's structure.

  • Components of Helium:

    • Valence Shell/Orbit: The outermost region of an atom where electrons reside.

Stability of Atoms

  • Octet Rule: A principle stating that atoms are stable when they have eight electrons in their valence shell.

    • Atoms with fewer than eight electrons in their outermost shell can be reactive.

    • Example: An atom with two electrons in the first shell and/or eight in the second or higher shells is considered stable and inert.

Concepts of Electronegativity

  • Electronegativity: The relative ability of an atom to attract electrons to itself when forming a bond.

    • Order of Electronegativity from Strongest to Weakest:

    • F (Fluorine)

    • O (Oxygen)

    • Cl (Chlorine)

    • N (Nitrogen)

    • C (Carbon)

    • H (Hydrogen)

    • Na (Sodium)

Interactions and Bonds

  • Types of Bonds:

    • Covalent Bonds: Bonds formed when atoms share electrons.

    • Polar Covalent Bonds: Electrons are shared unequally due to differences in electronegativity (e.g., H2O, NH3).

    • Nonpolar Covalent Bonds: Electrons are shared equally.

    • Ionic Bonds: Bonds formed when one atom donates electrons to another atom, resulting in the formation of cations and anions.

    • Example of Cation: Na⁺ (Sodium ion)

    • Example of Anion: Cl⁻ (Chloride ion)

  • Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.

  • Van der Waals Forces: Weak attractions between molecules or parts of molecules that result from transient local partial charges.

Properties of Molecules

  • Hydrophilic Molecules: Molecules that attract water (polar).

  • Hydrophobic Molecules: Molecules that repel water (nonpolar).

  • Effect of Electronegativity on Bonding: The proximity of an electronegative atom can create temporary dipoles, influencing molecular interactions.

Conclusion

  • Understanding atomic structure, electronegativity, and molecular interactions is crucial for studying biochemical processes and macromolecules in biology.