Biology 1310: Principles of Organic Chemistry

Introduction

• Start with organic chemistry as it is crucial for understanding biological macromolecules (Chapter 5 of the textbook).
• High school chemistry knowledge assumed.
• Extra resources: Chapters 2 & 3 of Campbell’s book, Khan Academy tutorials on CourseMoodle.

Six Key Points in Organic Chemistry

1. Covalent Bonds and Double Bonds

   • Organic compounds consist mainly of C, H, N, O, P, S.
   • Covalent bonds per element: C (4), H (1), N (3), O (2), P (3 or 5), S (2).
   • Importance of double bonds, e.g. in fatty acids (saturated vs unsaturated).
   • Double bonds impact molecular structure and physical properties (zigzag pattern in saturated fats, bends in unsaturated fats).

2. Electronegativity

   • Key concept: Elements' tendency to attract electrons in a bond.
   • Oxygen and Nitrogen are highly electronegative.
   • Non-polar bonds (equal sharing, e.g., methane) vs polar bonds (unequal sharing, e.g., water).
   • Concept of oxidation (losing electron proximity) and reduction (gaining electron proximity).
   • Importance of hydrogen bonds, especially in water’s properties and solubility.

3. Functional Groups in Organic Molecules

   • Carbon's ability to bond with different elements forms the basis of organic chemistry.
   • Important functional groups: Hydroxyl, Carboxyl, Carbonyl, Amino, Sulfhydryl, Phosphate, Methyl.
   • Functional groups give organic molecules their versatility and specific properties.

4. Numbering of Carbons

   • Carbon atoms in organic molecules are numbered for structure and naming.
   • IUPAC rules guide numbering; terminal carbon with a unique feature is often number 1.
   • Importance of numbering in macromolecules and nucleic acids.

5. Organic Chemistry Shorthand

   • Depictions often omit carbon atoms and hydrogens in diagrams.
   • Understanding shorthand helps in visualizing complex organic molecules.

6. Isomeric Forms of Organic Compounds

   • Structural isomers: Same formula, different bonding framework.
   • Stereoisomers: Same bonding framework, different orientation.
     • Enantiomers (mirror images, e.g., L and D forms of amino acids).
     • Cis-trans isomers (e.g., differences in glucose configurations affecting polymer properties).

Conclusion

• This foundational knowledge is essential for the upcoming sections on biological macromolecules.
• No direct examination on this material, but it will be relevant to future topics in the course.