Chemistry of Life - Organic Compounds and Macromolecules

Overview and Study Objectives

• Reading requirements:

  • Read all of Chapter 2 (Chemistry of Life) and pages 63–66 before reaching the "ENZYMES AND METABOLISM" section.

• Learning guidelines:

  • Comprehend all core terminology, specifically terms printed in bold text throughout the assigned reading.

  • Carefully study all figures and answer every "Before You Go On" section-ending question.

  • Complete end-of-chapter assessment sections:

  • Testing Your Recall

  • Building Your Medical Vocabulary

  • Testing Your Comprehension

Organic Compounds and Functional Groups

• Definition of organic compounds:

  • Organic compounds are defined as chemical compounds containing carbon.

• Major categories:

  • The four primary groups of organic molecules essential to life are:

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic acids

• Functional groups:

  • A functional group is defined as a specific group of atoms attached to a carbon skeleton that determines the chemical functional characteristics and reactive properties of an organic molecule.

• Key functional groups:

  • Hydroxyl group ($\text{-OH}$):

  • Structure: $\text{-OH}$

  • Occurrence: Sugars and alcohols.

  • Methyl group ($\text{-CH}_3$):

  • Structure: $\text{-CH}_3$

  • Occurrence: Fats, oils, steroids, and amino acids.

  • Carboxyl group ($\text{-COOH}$):

  • Structure: $\text{-COOH}$

  • Occurrence: Amino acids, sugars, and proteins.

  • Amino group ($\text{-NH}_2$):

  • Structure: $\text{-NH}_2$

  • Occurrence: Amino acids and proteins.

  • Phosphate group ($\text{-H}_2\text{PO}_4$):

  • Structure: $\text{-H}_2\text{PO}_4$

  • Occurrence: Nucleic acids and adenosine triphosphate (ATP).

Adenosine Triphosphate (ATP) Structure

• Chemical classification and structure:

  • Adenosine Triphosphate (ATP) is a nucleotide compound consisting of three major structural subunits:

  • A nitrogenous base: Adenine.

  • A five-carbon sugar: Ribose ($\text{C}_5\text{H}_{10}\text{O}_5$).

  • Three phosphate groups attached in series to the ribose sugar ($\text{-PO}_4^-\text{-PO}_4^-\text{-PO}_4^-$).

Monomers, Polymers, and Reaction Mechanisms

• Polymers and Monomers:

  • Polymers are large organic molecules constructed from a repetitive series of identical or similar structural units called monomers.

  • Example: Starch is a polymer composed of approximately $3,000$ glucose monomers linked together.

• Polymerization and Synthesis Reactions:

  • Polymerization is the chemical process through which individual monomers are bonded together to form a polymer.

  • Polymerization occurs via dehydration synthesis (also termed a condensation reaction):

  • A hydrogen ion ($\text{H}^+$) is removed from one monomer, and a hydroxyl group ($\text{OH}^-$) is removed from another monomer.

  • These combine to produce a water molecule ($\text{H}_2\text{O}$), creating a covalent bond between the two monomers to generate a dimer or extended polymer chain.

• Hydrolysis Reactions:

  • Hydrolysis is the cleavage reaction opposite to dehydration synthesis.

  • A water molecule ($\text{H}_2\text{O}$) is split into $\text{H}^+$ and $\text{OH}^-$, breaking a covalent bond in a dimer or polymer and restoring individual monomer molecules.

Carbohydrates

• Physical and chemical properties:

  • Carbohydrates are hydrophilic molecules because they possess numerous polar hydroxyl ($\text{-OH}$) functional groups that readily form hydrogen bonds with water.

  • General empirical formula: $(\text{CH}_2\text{O})_n$, where $n$ represents the number of carbon atoms.

• Monosaccharides (Simple Sugars):

  • Monosaccharides are single-sugar monomers with the molecular formula $\text{C}_6\text{H}_{12}\text{O}_6$.

  • Glucose, galactose, and fructose are structural isomers of one another, sharing the molecular formula $\text{C}_6\text{H}_{12}\text{O}_6$ but differing in structural arrangement.

• Disaccharides:

  • Disaccharides consist of two monosaccharide units joined covalently by dehydration synthesis:

  • Sucrose: Table sugar, composed of Glucose + Fructose.

  • Lactose: Milk sugar, composed of Glucose + Galactose.

  • Maltose: Product of starch digestion, composed of Glucose + Glucose.

• Polysaccharides:

  • Polysaccharides are long chains composed of repeating glucose monomers.

  • Glycogen:

  • An energy-storage polysaccharide synthesized in animals and humans.

  • Features a highly branched chain structure composed of repeating glucose units ($\text{Glu}-\text{Glu}-\text{Glu}$).

• Starch:

  • Energy-storing polysaccharide in plants; utilized when sunlight and nutrients are unavailable.

• Cellulose:

  • Structural polysaccharide found in plant cell walls (e.g., wood, cotton).

  • Human digestive enzymes cannot hydrolyze cellulose bonds, making it an indigestible dietary fiber.

  • Conjugated Carbohydrates:

• Carbohydrates covalently bonded to proteins or lipids:

  • Glycolipids: Carbohydrates bound to lipids, forming key structural components of the cell surface coat (glycocalyx).

  • Glycoproteins: Carbohydrates bound to proteins, serving as a major component of mucus.

  • Proteoglycans: Large complexes containing carbohydrates and proteins that hold cells and tissues together, form the gelatinous filler within the eye, and provide lubrication in joints.

Lipids and Triglyceride Synthesis

• General characteristics:

  • Lipids are hydrophobic molecules with a high ratio of hydrogen to oxygen compared to carbohydrates (e.g., tristearin formula $\text{C}_{57}\text{H}_{110}\text{O}_6$ versus carbohydrate general formula $(\text{CH}_2\text{O})_n$).

  • Lipids are less oxidized than carbohydrates, enabling them to yield significantly more calories per gram.

• Major Lipid Types and Functions:

• Fatty acids: Precursor of triglycerides; direct source of energy. Fatty acids are either saturated (no carbon-carbon double bonds, e.g., Palmitic acid $\text{CH}_3(\text{CH}_2)_{14}\text{COOH}$, Stearic acid $\text{CH}_3(\text{CH}_2)_{16}\text{COOH}$) or unsaturated (contains carbon-carbon double bonds, e.g., Linoleic acid $\text{CH}_3(\text{CH}_2)_4\text{CH}=\text{CHCH}_2\text{CH}=\text{CH}(\text{CH}_2)_7\text{COOH}$).

• Triglycerides: Composed of a glycerol molecule bonded to three fatty acid chains. Functions include energy storage, thermal insulation, filling space, binding organs together, and cushioning organs.

• Phospholipids: Major structural components of cell membranes and assistance in fat digestion.

• Eicosanoids: Function as chemical messengers between cells.

• Fat-soluble vitamins: Involved in various functions including blood clotting, wound healing, vision, and calcium absorption.

• Cholesterol: Component of cell membranes and precursor of all other steroids.

• Steroid hormones: Function as chemical messengers between cells.

• Bile acids: Steroids that aid in fat digestion and nutrient absorption.

  • Synthesis of Triglycerides:

• Reaction type: Dehydration synthesis reaction combining one glycerol molecule with three fatty acid molecules, producing one triglyceride molecule and three water molecules ($3\,\text{H}_2\text{O}$).

Phospholipids and Steroids

• Phospholipid Structure (e.g., Lecithin):

  • Amphipathic structure consisting of:

  • A hydrophilic head region containing a nitrogen-containing group (choline), a phosphate group ($\text{-PO}_4^-$), and glycerol.

  • A hydrophobic tail region containing two fatty acid chains.

• Cholesterol and Steroid Structure:

  • All steroids share a basic four-ringed carbon backbone structure.

  • Cholesterol ($\text{C}_{27}\text{H}_{46}\text{O}$) is a natural lipid product found exclusively in animal tissue.

• Clinical & Functional Implications:

  • Essential precursor for synthesizing all other steroids (e.g., steroid hormones, bile acids).

  • Important structural component of cellular membranes.

  • Implicated in cardiovascular disease risk profiles.

Amino Acids, Peptides, and Protein Structure

• Basic Amino Acid Structure:

  • A protein is a polymer composed of amino acid monomers.

  • Each amino acid consists of a central carbon atom bonded to:

  • An amino group ($\text{-NH}_2$).

  • A carboxyl group ($\text{-COOH}$).

  • A hydrogen atom ($\text{-H}$).

  • A variable side chain or radical group ($\text{-R}$), which defines the unique chemical properties of each of the $20$ natural amino acids.

  • Amino acid side chains ($\text{-R}$ groups) vary in polarity and charge:

  • Nonpolar amino acids: e.g., Methionine ($\text{-CH}_2\text{-CH}_2\text{-S-CH}_3$).

  • Polar amino acids: e.g., Cysteine ($\text{-CH}_2\text{-SH}$), Tyrosine ($\text{-CH}_2\text{-C}_6\text{H}_4\text{-OH}$), Arginine ($\text{-(CH}_2)_3\text{-NH-C(NH}_2)^+=\text{NH}_2$).

• Peptide Bond Formation:

  • Amino acids are joined together via covalent peptide bonds through dehydration synthesis.

  • The carboxyl group ($\text{-COOH}$) of one amino acid reacts with the amino group ($\text{-NH}_2$) of another amino acid, releasing a water molecule ($\text{H}_2\text{O}$) to form a dipeptide.

• Hierarchical Levels of Protein Structure:

  • Primary Structure:

  • The sequence of amino acids linked by peptide bonds in a linear chain.

  • Example: Primary sequence of insulin, composed of two disulfide-linked polypeptide chains.

• Secondary Structure:

  • Local folding patterns formed by hydrogen bonding between backbone groups, producing $\alpha$-helices or $\beta$-pleated sheets.

• Tertiary Structure:

  • Three-dimensional folding and coiling resulting from interactions among radical ($\text{-R}$) groups and between $\text{-R}$ groups and surrounding water molecules.

  • Globular proteins: Compact, ball-like shapes (e.g., enzymes, antibodies).

  • Fibrous proteins: Slender filaments adapted for contraction and structure (e.g., muscle contractile proteins).

• Quaternary Structure:

  • Spatial association and assembly of two or more individual polypeptide chains (subunits) into a functional protein complex (e.g., hemoglobin composed of two $\alpha$ chains and two $\beta$ chains surrounding heme groups).

Biological Functions of Proteins

• Structural support:

  • Keratin gives structural strength to nails, hair, and the skin surface.

• Cellular communication:

  • Peptide ligands bind to specific receptor proteins (e.g., oxytocin binding to its membrane receptor).

• Membrane transport:

  • Transmembrane channels facilitate solute passage (e.g., sodium $\text{Na}^+$ and potassium $\text{K}^+$ channels).

• Biological catalysis:

  • Enzymes act as biological catalysts to accelerate chemical reactions.