Introduction to Organic Chemistry and Related Biomolecules

ORGANIC CHEMISTRY

  • Definition: Organic chemistry is the study of carbon compounds.

    • Organic Molecules: Composed of carbon and typically contain hydrogen and oxygen.

    • Historical Context: Originally focused on compounds derived from living organisms (the concept of “vitalism”), which was refuted in the early 1800s.

    • Contrast with Inorganic Chemistry: Inorganic chemistry studies compounds from nonorganic matter; inorganic molecules may or may not contain carbon.

  • Diversity of Compounds: There are significantly more known organic compounds than inorganic compounds.

  • Major Groups of Biomolecules: Four primary categories of organic molecules are studied:

    1. Carbohydrates

    2. Lipids

    3. Proteins

    4. Nucleic acids

    • Each group shares common characteristics but varies in specific properties.

I. CARBOHYDRATES

  • Definition and Formula: Carbohydrates typically have the empirical formula of CnH{2n}On , which can also be expressed as (CH2O)_n with notable exceptions.

    • Nomenclature: Carbohydrates often end with the suffix “-ose,” examples include sucrose, lactose, and glucose.

    • Proportion of Organic Matter: Approximately 50% of all organic matter on Earth consists of carbohydrates.

    • Role in Energy: The carbon bonds in carbohydrates release energy upon breakdown, which most living organisms can utilize.

  • Structural Units: The basic structural unit for carbohydrates is the saccharide (or sugar).

    • Monosaccharides: A carbohydrate containing a single structural unit, cannot be reduced to simpler sugars; typically composed of 3 to 7 carbon atoms. Common examples include:

    • Hexoses: Glucose and fructose, both containing 6 carbon atoms.

    • Disaccharides: Formed from the joining of two monosaccharides through dehydration synthesis, resulting in the elimination of a water molecule. Examples include:

    • Sucrose: Formed from glucose and fructose by dehydration.

    • Hydrolysis: The reverse reaction which uses water to split a disaccharide back into two monosaccharides (e.g., glucose and fructose).

    • Maltose: A disaccharide formed by the dehydration of two glucose molecules.

    • Polysaccharides: Composed of multiple monosaccharides joined together after dehydration. They are significant storage forms of carbohydrates, examples include:

    • Starch: The main storage molecule in plants, which is not readily soluble in water, making it efficient for energy storage.

    • Glycogen: Similar to starch but found in animals, specifically in the liver and skeletal muscle cells.

II. LIPIDS

  • Definition: Lipids are complex organic molecules that are generally insoluble in water (hydrophobic) due to their nonpolar nature.

    • Categories of Lipids:

    1. Neutral fats (triglycerides)

    2. Phospholipids

    3. Steroids

    4. Other lipoid substances

  • Neutral Lipids: Composed of glycerol and three fatty acids; they provide an excellent storage medium for high-energy molecules due to their insolubility in water.

  • Phospholipids: Structurally similar to neutral lipids, but have one fatty acid replaced by a phosphate group. Characteristics:

    • Dual Properties: Contain both hydrophilic (water-attracting) and hydrophobic (water-repelling) regions due to the polar phosphate group.

    • Function: Major components of cell membranes, forming a bilayer:

    • Hydrophilic Heads: Point towards the watery environment inside and outside the cell.

    • Hydrophobic Tails: Are sandwiched between the hydrophilic heads, creating a semi-permeable membrane.

  • Steroids: Structurally distinct as they comprise four interlocking hydrocarbon rings; examples include:

    • Cholesterol

    • Bile salts

    • Vitamin D

    • Various hormones

  • Other Lipoid Substances: Include fat-soluble vitamins (A, E, K), eicosanoids (derived from arachidonic acid, such as prostaglandins, leukotrienes, and thromboxanes), and lipoproteins.

III. PROTEINS

  • Definition: Proteins are crucial organic molecules that serve both structural and functional roles in the body.

    • Building Blocks: Comprised of amino acids (approximately 20 naturally occurring types).

  • Structure of Amino Acids:

    • Each amino acid has:

    • Amine Group: -NH_2

    • Carboxyl Group: -COOH (the organic acid).

    • R Group: A specific group that varies among amino acids, determining their unique properties.

  • Linking Amino Acids: Two amino acids are bonded through a dehydration synthesis reaction, where water is removed to form a peptide bond. This process results in a polypeptide chain when multiple amino acids are linked.

    • Proteins Structure: Consist of one or more polypeptide chains, which fold into specific functional shapes.

IV. pH AND BUFFERS

  • Acids and Bases:

    • Acid Definition: A substance that increases the concentration of hydrogen ions ( H^+ ) in a solution.

    • Base Definition: A substance that decreases hydrogen ion concentration, equivalently increasing hydroxyl ion ( OH^- ) concentration.

  • pH Measurement: The pH scale measures the relative concentration of hydrogen ions versus hydroxide ions in a solution.

    • pH Scale Range: 0 (acidic) to 14 (basic), where 7.0 is neutral.

    • pH Interpretation:

    • Acidic Solution: pH < 7 (more H^+ than OH^- ).

    • Basic Solution: pH > 7 (more OH^- than H^+ ).

  • Blood pH: Maintains a range of 7.35 - 7.45 , identifying it as slightly basic.

    • Metabolic Processes: Often produce acidic products; deviation from blood pH can have serious effects.

  • Buffer Function:

    • Definition: A buffer is a substance that helps maintain stable pH levels by absorbing excess hydrogen ions or releasing them when needed, referred to as a “chemical sponge.”