Biology Module 2: Biomolecules Study Notes

3.1 Organic Molecules

• Definition: Organic molecules unequivocally contain both carbon (C) and hydrogen (H) atoms.

• Four Classes of Organic Molecules (Biomolecules): These are the fundamental molecules forming the basis of living organisms:

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic Acids

• Diverse Functions: The functions of these biomolecules within the cell are extremely diverse and critical for life.

• Carbon and Life (Figure 3.1):

  • Carbon forms the essential basis of life as it is currently understood.

  • Examples of Carbon's Structural Role:

    • (a) Lipids: Store energy, illustrated by the lipids in a canola plant.

    • (b) Carbohydrates: Provide structural support, evident in the cellulose that gives structure to a tree.

    • (c) Proteins: Form vital components such as hemoglobin in red blood cells.

    • (d) Nucleic Acids: Constitute the genetic material, exemplified by the DNA passed from a lioness to her offspring.

• The Carbon Atom's Properties:

  • Covalent Bonding: A carbon atom is capable of forming four covalent bonds.

  • Bonding Partners: Carbon can form stable bonds with other carbon atoms, as well as with nitrogen, hydrogen, oxygen, phosphorus, and sulfur.

  • C-C Bond Stability: The carbon-carbon (C-C) bond is exceptionally stable.

  • Hydrocarbons: Long chains composed solely of carbon and hydrogen atoms, known as hydrocarbons, can be formed.

  • Variety of Bonds and Structures: Beyond single bonds, carbon can form double bonds (C=C), triple bonds, and various stable ring structures.

  • Complexity through Branching: Branches can form at any carbon atom, facilitating the formation of highly complex carbon chains.

• The Carbon Skeleton and Functional Groups:

  • Carbon Skeleton (Backbone): This term refers to the continuous carbon chain that forms the fundamental framework of an organic molecule.

  • Functional Groups: These are specific clusters of atoms that are bonded to the carbon skeleton and possess distinct structures and characteristic chemical functions.

    • Determinant of Properties: Functional groups are crucial because they determine the chemical reactivity and polarity of organic molecules.

    • Table 3.1 Functional Groups:

      • Hydroxyl (R-OH):

        • Compound Type: Alcohol (e.g., ethanol).

        • Significance: Highly polar, capable of forming hydrogen bonds. Present in sugars and certain amino acids.

      • Carbonyl (C=O):

        • Aldehyde (R-CHO):

          • Compound Type: Formaldehyde.

          • Significance: Polar. Found in sugars.

        • Ketone (R-CO-R'):

          • Compound Type: Acetone.

          • Significance: Polar. Also found in sugars.

      • Carboxyl (R-COOH) (Acidic):

        • Compound Type: Carboxylic acid (e.g., acetic acid).

        • Significance: Polar and acidic (can donate a proton). Present in fatty acids and amino acids.

      • Amino (R-NH_2):

        • Compound Type: Amine (e.g., tryptophan).

        • Significance: Polar, basic (can accept a proton), and forms hydrogen bonds. Present in amino acids.

      • Sulfhydryl (R-SH):

        • Compound Type: Thiol (e.g., ethanethiol).

        • Significance: Crucial for forming disulfide bonds (S-S), which stabilize protein structure. Present in certain amino acids (e.g., cysteine).

      • Phosphate (R-O-PO3H2):

        • Compound Type: Organic phosphate (e.g., phosphorylated molecules).

        • Significance: Polar and acidic. Key component of nucleotides and phospholipids.

• Isomers (Figure 3.2):

  • Definition: Isomers are organic molecules that share an identical molecular formula but differ in the spatial arrangement of their atoms.

  • Example: Both glyceraldehyde and dihydroxyacetone share the molecular formula C3H6O_3.

    • Glyceraldehyde: A colorless crystalline solid where the oxygen atom is double-bonded to an end carbon atom.

    • Dihydroxyacetone: A white crystalline solid where the oxygen atom is double-bonded to the middle carbon atom.

    • Despite the same formula, their different atomic configurations result in distinct chemical and physical properties.

The Biomolecules of Cells

• Four Primary Classes: The four classes of biomolecules are Carbohydrates, Lipids, Proteins, and Nucleic acids.

• Monomers and Polymers: Most biomolecules are built from repeating units.

  • Monomers: These are single, small repeating units (e.g., amino acids).

  • Polymers: A molecule composed of many linked monomer units (meaning