2.5 Chapter 2 Summary

2.1 Atoms, Ions, and Molecules

• Atoms are composed of protons, neutrons, and electrons. The number of protons defines the element; electrons in the outer shell determine chemical behavior.

• Isotopes have varying neutron numbers but similar chemical properties.

• Ions form when atoms gain or lose electrons, becoming charged (cations: positive, anions: negative).

• Molecules are two or more atoms held together by chemical bonds. Biological molecules include water, salts, organic compounds, etc.

2.2 Covalent Bonds and Other Molecular Interactions

• Covalent bonds involve sharing electron pairs.

  • Nonpolar covalent: equal sharing (e.g., O₂, CH₄).

  • Polar covalent: unequal sharing due to electronegativity differences (e.g., H₂O)

• Electronegativity determines bond polarity; greater differences lead toward ionic character.

• Ionic bonds form when electrons transfer fully, creating oppositely charged ions.

• Non-covalent interactions:

  • Hydrogen bonds: weak attractions between atoms with a partial positive charge and atoms with a partial negative charge, crucial for water’s properties, protein folding, DNA stability

  • Van der Waals forces: transient attractions due to temporary dipoles between atoms forming nonpolar covalent bonds.

  • These weaker forces significantly contribute to macromolecular structure and function.

2.3 Water

• Polarity & hydrogen bonding: H₂O’s bent shape and polar bonds create dipoles, enabling extensive hydrogen bonding between molecules.

• Unique properties:

  • High melting/boiling points, surface tension, heat capacity, and cohesion due to H-bonds

  • Ice forms an open, hydrogen-bonded lattice—making it less dense than liquid water.

• Biological roles:

  • Universal solvent: dissolves hydrophilic molecules and impacts biochemical interactions.

  • Thermal stability supports enzyme function and climate buffering.

• Dynamic network: Bonds continually form and break in picoseconds, yet collectively shape water’s macroscopic behavior .

2.4 Carbon

• Fundamental to life: Carbon’s four valence electrons allow up to four covalent bonds, enabling diverse structures

• Hydrocarbons: Chains or rings of C and H (e.g., methane, propane) store significant energy and serve as fuel.

• Bond variety: Single, double, and triple C–C bonds influence molecular geometry and reactivity.

• Isomers: Molecules with the same formula but different structure, leading to varied properties (structural, cis-trans).

• Enantiomers: Mirror-image molecules not superimposable (e.g., L- and D-amino acids); often only one form (usually L) is biologically active

• Functional groups: Common reactive attachments on carbon backbones include hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, sulfhydryl. They confer specific chemical traits—hydrophilic, hydrophobic, acidic, basic—and mediate macromolecule activity and interactions

🔗How These Chapters Interconnect:

• From atoms → life: Building blocks (atoms & ions) form molecules via bonds; carbon chemistry provides the backbone of diverse biological macromolecules.

• Interactions shape biology: Non-covalent forces (H‑bonds, van der Waals) and water’s polarity determine structure, function, and interactions in cells.

• Functional diversity: Carbon’s bonding versatility and functional groups enable the complexity of proteins, nucleic acids, lipids, and carbohydrates.

Summary was initially generated by ChatGPT then modified by the author.