Carbon & Organic Molecules (Ch. 2.4–2.5 + Lecture)

1. Why Carbon is the Basis of Life

  • Abundance in cells: C, H, O, N = ~90% of cell dry mass; carbon most abundant.

  • Unique versatility:

    • 4 valence electrons → forms 4 covalent bonds.

    • Geometry = tetrahedron → structural variety.

    • Single bonds = free rotation → flexibility.

    • Bonds with itself → chains, branches, rings.

    • Double bonds = shorter, rigid, planar (no rotation).

  • Isomers: Same chemical formula, different structure (e.g., leucine vs isoleucine).

  • Silicon vs. Carbon: Both can make 4 bonds, but silicon is locked to oxygen → far less diversity. Life elsewhere would almost certainly also be carbon-based.

2. Four Classes of Macromolecules

  1. Proteins

    • Functions: enzymes (catalysts), structure, transport, movement.

    • Monomer: amino acid (20 types).

    • Polymer: polypeptide/protein.

    • Bond: peptide bond (C–N).

    • Built by dehydration reaction (removes H2O).

    • Properties depend on R-group side chain.

  2. Nucleic Acids (DNA & RNA)

    • Functions: store & transmit genetic info, regulate gene expression.

    • Monomer: nucleotide = sugar (ribose or deoxyribose) + base + phosphate group.

    • Polymer: DNA or RNA.

    • Bond: phosphodiester bond.

    • DNA bases: A–T, G–C (complementary hydrogen bonds).

    • RNA bases: A–U, G–C.

    • DNA = double helix with sugar–phosphate backbone outside, bases inside.

  3. Carbohydrates

    • Functions: quick energy, storage, structural support (cell walls).

    • Formula ratio: C:H:O ≈ 1:2:1.

    • Monomer: monosaccharide (glucose, galactose, fructose).

    • Bonds: glycosidic bonds (release H2O).

    • Polymers: polysaccharides (starch, glycogen, cellulose, pectin).

    • Forms:

      • Aldose sugars = aldehyde group (HC=O).

      • Ketose sugars = ketone group (C=O).

      • Usually form ring structures in water.

    • Complex carbs: long, branched chains of sugars → diverse functions.

  4. Lipids (not polymers — defined by hydrophobicity)

    • Functions: membranes, energy storage, signaling (hormones).

    • Types:

      1. Triacylglycerols (fats/oils)

        • Glycerol + 3 fatty acids.

        • Saturated fatty acids: no double bonds, straight, solid at room temp.

        • Unsaturated fatty acids: ≥1 double bond, kinks, liquid at room temp.

        • Held by van der Waals forces → melting point depends on chain length & saturation.

      2. Steroids

        • 4 fused carbon rings.

        • Examples: cholesterol (membranes), estrogen/testosterone.

      3. Phospholipids

        • Glycerol + 2 fatty acids + phosphate group.

        • Amphipathic: hydrophobic tails + hydrophilic head.

        • Form bilayers → cell membranes.

3. Functional Groups (Molecular “Personalities”)

(From lecture + Table 2.1)

Functional Group

Formula

Properties

Found In

Amino

–NH₂

Polar, basic, + charged at cell pH, hydrophilic

Amino acids, proteins

Amide

–C(=O)–NH–

Polar, hydrophilic

Proteins

Carboxyl

–COOH

Polar, acidic, – charged at cell pH, hydrophilic

Fatty acids, proteins

Carbonyl

>C=O

Polar, hydrophilic, non acidic

Carbohydrates, proteins

Hydroxyl

–OH

Polar, hydrophilic, no acidic

Carbs, proteins, nucleic acids

Sulfhydryl

–SH

Polar, forms disulfide bonds

Cysteine, proteins

Methyl

–CH₃

Nonpolar, hydrophobic

Amino acids, proteins, DNA

Phosphate

–OPO₃H₂

Polar, – charged, hydrophilic

Nucleic acids, ATP, phospholipids

➡ Functional groups make otherwise nonpolar molecules polar, soluble, and reactive.
➡ Reactions (like dehydration) occur between functional groups.

4. Key Chemical Reactions

  • Dehydration synthesis (condensation):

    • Joins monomers → polymers.

    • Removes H₂O.

    • Example: peptide bond (protein), glycosidic bond (carbs), phosphodiester bond (DNA).

  • Hydrolysis:

    • Breaks polymers → monomers.

    • Adds H₂O.

    • Example: digestion of starch → glucose.

5. Simplified Quick Review

  • Carbon = 4 bonds, tetrahedral, versatile → life’s backbone. non-polar molecules do not mix well with water, leading to the formation of lipid bilayers in cell membranes.

  • Proteins = amino acids, peptide bonds, enzymes & structure

  • Nucleic Acids = nucleotides, phosphodiester bonds, DNA/RNA info, sugar

  • Carbohydrates = monosaccharides, glycosidic bonds, energy & structure.

  • Lipids = hydrophobic, fats/oils, phospholipids, steroids, store energy, nutrolipids

  • Functional groups = determine reactivity & solubility.

  • Dehydration vs Hydrolysis = build vs break polymers.

In-class

H bonds are weaker and covalent bonds are stronger

when carbon is bond to carbon it is non-polar

electronegativity - how big the atoms is (O and N are highly electronegative) ( C and H are not)

a bond is polar if it is hydrophilic (soluble in water )

non polar if it hydrophobic (not soluble in water)

solid line are covalent bonds

dotted line h-bonds

in tree chart lable it (chemical linkages)