Chapter 3

Introduction to Organic Molecules

  • Overview of Organic Molecules
    • There are four major classes of large organic molecules in biological systems: carbohydrates, proteins, lipids, and nucleic acids.

Structure and Representation of Carbon

  • Carbon Structure

    • Carbon can be represented in various structural forms:
    • Standard notation: uses the letter "C" to denote carbon atoms and indicates bonding.
    • Structural formula: angles represent bonded carbon atoms, where each vertex corresponds to a carbon atom.
    • Bonding Types:
    • Double Bonds: Indicated by double lines between two carbon atoms.
    • Single Bonds: Represented by single lines between carbon atoms.

  • Examples of Carbon Structures:

    • Gasoline and Hydrocarbons:
    • Octane (C8H18) and hexane (C6H14) are examples.
    • Octane is used in cars for better performance; higher octane number implies anti-knocking properties, resulting in increased horsepower.
    • Energy from breaking these structures can lead to ignition, creating high energy release, which is dangerous when handled improperly.

Functional Groups in Organic Molecules

  • Hydrogens vs. Functional Groups

    • Instead of solely hydrogen attached to carbon atoms, functional groups can be introduced, altering chemical behavior significantly.
    • Common Functional Groups:
    • Hydroxyl (-OH)
    • Carbonyl (C=O)
    • Amino (-NH2)
    • Phosphate (-PO4)
    • Methyl (-CH3)

  • Role of Functional Groups:

    • They confer specific chemical properties on the organic molecules and play vital roles in biochemical processes, such as protein formation (e.g. amino groups for peptides).

Monomers and Polymers

  • Monomers:

    • Basic units that make up larger structures; vital in constructing polymers.
    • Examples:
      • Carbohydrates: Made of monosaccharides (e.g., glucose).
      • Proteins: Composed of amino acids.
      • Lipids: Consist of fatty acids and glycerol.
      • Nucleic Acids: Made of nucleotides.

  • Polymerization:

    • Monomers link together to form polymers through various chemical reactions, which may include condensation (dehydration) or hydrolysis reactions.

Carbohydrates

  • Monomer:

    • Monosaccharides, e.g., glucose, fructose.

  • Polysaccharides:

    • Formed by linking multiple monosaccharides:
    • Examples include starch (found in potatoes) and glycogen (an animal storage form).
    • Chemical Behavior:
    • Glycogen is stored in muscle tissues, providing quick energy access during activities.
    • Carbohydrates are primary energy sources and are stored in various forms.

Lipids

  • Components:

    • Comprised of fatty acids and glycerol.
    • Types of fatty acids include saturated, unsaturated, and trans fats.

  • Triglycerides:

    • Most common form of lipids. Comprised of three fatty acids esterified to glycerol.
    • Serve critical roles in energy storage, insulation, and cellular structures.

Proteins

  • Monomer:

    • Amino acids (20 standard types including 9 essential and 11 non-essential amino acids).

  • Structure:

    • Proteins possess four structural levels:
    • Primary Structure: Sequence of amino acids in a polypeptide chain.
    • Secondary Structure: Hydrogen bonding leads to alpha helices and beta pleated sheets.
    • Tertiary Structure: 3D structure formed from interactions among various amino acid side chains.
    • Quaternary Structure: Multiple polypeptide chains (subunits) come together to form a functional protein, e.g., hemoglobin.

  • Denaturation:

    • Proteins can lose their structure and function when exposed to extreme temperature changes or chemicals, resulting in loss of active structure without breaking peptide bonds.

Enzymes

  • Definition:

    • Enzymes are biological catalysts which speed up the rate of chemical reactions and lower the activation energy required for reactions.

  • Active Site:

    • The specific region of the enzyme where the substrate binds; shape and chemical properties directly influence enzyme specificity and catalytic efficiency.

Nucleic Acids

  • Types:

    • DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid).

  • Nucleotides:

    • Composed of a sugar (deoxyribose for DNA, ribose for RNA), phosphate group, and nitrogenous base.
    • Bases in DNA: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).
    • Bases in RNA: Adenine (A), Uracil (U), Cytosine (C), Guanine (G).
    • Base Pairing: A-T (or A-U in RNA) and C-G.

  • Structure:

    • DNA forms a double helix structure with a sugar-phosphate backbone and nitrogen bases forming the rungs of the ladder.

  • Function:

    • Carries genetic information; sequences code for proteins, influencing traits.

ATP - Adenosine Triphosphate

  • Role in Energy Transfer:

    • ATP acts as the energy currency of cells; energy is released when phosphate groups are broken off (ATP to ADP).

  • Structure:

    • Composed of an adenosine molecule bonded to three phosphate groups.

Summary of Key Points

  • Each of the four major classes of organic molecules (carbohydrates, lipids, proteins, nucleic acids) plays essential roles in biological systems and is made up of smaller monomers that undergo polymerization.
  • Understanding the structure, function, and interactions of these molecules is foundational for studying biology and biochemistry.