Organic Molecules

Chapter 3: Organic Molecules

• Organic molecules contain carbon and are abundant in living organisms.

• Macromolecules are large, complex organic molecules (e.g., polysaccharides).

The Carbon Atom

• Carbon has 4 electrons in its outer shell and can form up to 4 bonds (usually single or double).

• Carbon can form nonpolar or polar bonds.

  • Molecules with polar bonds are water-soluble (hydrophilic).

  • Molecules with nonpolar bonds (e.g., hydrocarbons) are not very water-soluble (hydrophobic).

Functional Groups

• Groups of atoms with special chemical features that are functionally important.

• Each type exhibits the same properties in all molecules in which it occurs.

Isomers

• Two molecules with an identical molecular formula but different structures and characteristics.

  • Structural isomers: same atoms but different bonding relationships.

  • Stereoisomers: identical bonding relationships, but spatial positioning differs.

    • Cis-trans isomers: variable positioning of atoms around a double bond.

    • Enantiomers: mirror image molecules.

Polymers and Monomers

• Polymer: many parts; a long molecule made of repeating units called monomers.

• Monomer: one part; a small molecule that attaches to another monomer to build a polymer.

Formation of Organic Molecules

• Dehydration reaction (condensation reaction): links monomers to form polymers by removing a water molecule.

Breakdown of Organic Molecules

• Hydrolysis reaction: Polymers are broken down into monomers by adding a water molecule.

4 Main Types of Macromolecules

• Carbohydrates, Lipids, Proteins, and Nucleic Acids.

Carbohydrates

• Composed of carbon, hydrogen, and oxygen atoms. General formula is Cn(H2O)_n.

Monosaccharides

• Simplest sugars. Common types include:

  • Pentoses (5 carbons): Ribose (C5 H10 O5$), Deoxyribose ($ C5 H10 O4

  • Hexoses (6 carbons): Glucose (C6 H12 O6),

• Exist in linear (less common) and ring (most common) structures in biological solutions.

Stereoisomers (Carbohydrates)

• $α$ glucose vs. $β$ glucose: Hydroxyl group of carbon 1 is below or above the ring.

Enantiomers (Carbohydrates)

• $β$-D- and $β$-L-glucose: Mirror image structure. $β$-D-glucose is used in biological systems.

Disaccharides

• Two monosaccharides bonded together by dehydration, forming a glycosidic bond.

• Broken apart by hydrolysis. Examples: sucrose, maltose, lactose.

Polysaccharides

• Many monosaccharides linked to form long polymers.

  • Energy storage: starch (plants), glycogen (animals).

  • Structural: cellulose (plants), chitin (animals and fungi), glycosaminoglycans (extracellular matrix).

Lipids

• Predominantly hydrogen and carbon atoms; nonpolar and insoluble in water.

Fats

• Triglycerides (triacylglycerols): glycerol bonded to 3 fatty acids via dehydration (ester bond).

Fatty Acids

• Saturated: all carbons linked by single bonds; solid at room temperature.

• Unsaturated: one or more double bonds; liquid at room temperature (oils).

  • Cis forms naturally; trans formed artificially (linked to disease).

Phospholipids

• Amphipathic molecules with a polar (hydrophilic) head and nonpolar (hydrophobic) fatty acid tails.

• Form lipid bilayers in plasma membranes.

Steroids

• Four interconnected rings of carbon atoms, usually insoluble in water. Example: cholesterol.

Proteins

• Composed of carbon, hydrogen, oxygen, nitrogen, and sulfur.

• Building blocks are amino acids (20 different types), each with a common structure and variable side chain (R group).

Amino Acid Structure

• Amino group (positively charged at neutral pH) and carboxyl group (negatively charged at neutral pH). R groups are:

  • Nonpolar: glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, cysteine, methionine.

  • Polar and uncharged: serine, threonine, asparagine, glutamine, tyrosine.

  • Polar and charged: aspartic acid, glutamic acid, histidine, lysine, arginine.

Polypeptide Formation

• Amino acids joined by dehydration reactions forming peptide bonds.

• Polymers of amino acids are polypeptides, broken down by hydrolysis.

Polypeptide Structure

• Has an N-terminus (amino end) and a C-terminus (carboxyl end).

Protein Structure

• Primary: linear sequence of amino acids.

• Secondary: amino acid sequences forming hydrogen bonds -
  $α$-helices or $β$-sheets.

• Tertiary: 3D shape from folding of secondary structures and random coils.

• Quaternary: two or more polypeptides binding to form a functional protein.

Factors Promoting Protein Folding and Stability

• Hydrogen bonds, ionic bonds, hydrophobic effects, van der Waals forces, disulfide bridges.

Protein-Protein Interactions

• Specific binding at the surface using hydrogen bonds, ionic bonds, hydrophobic effects, and van der Waals forces.

Nucleic Acids

• Long polymers of nucleotides; responsible for storage, expression, and transmission of genetic information.

  • DNA: stores genetic information.

  • RNA: decodes DNA to build polypeptide chains.

Nucleotides

• Composed of a phosphate group, a five-carbon sugar (ribose or deoxyribose), and a nitrogenous base.

• Linked into a polymer via a sugar-phosphate backbone.

DNA Structure

• Two strands of nucleotides coiled in a double helix, held by hydrogen bonds between purine and pyrimidine bases.

  • A pairs with T; G pairs with C.

DNA vs RNA

• DNA: deoxyribonucleic acid, deoxyribose sugar, thymine (T), double helix.

• RNA: ribonucleic acid, ribose sugar, uracil (U), single strand.