Organic compounds

Chapter 3: The Chemistry of Life: Organic Compounds

Organic Compounds

• Definition: Covalently bonded carbon atoms form the backbone of organic molecules.

• Carbon's Versatility:

  • Carbon forms bonds with more different elements than any other atom.

  • Over five million organic compounds identified, including large macromolecules made from modular subunits.

Carbon Atoms and Organic Molecules

• Covalent Bonds:

  • A carbon atom can complete its valence shell by forming four covalent bonds.

  • Carbon-to-carbon bonds are strong and stable, not easily broken.

  • Three types of carbon-to-carbon bonds:

  1. Single bonds

  2. Double bonds

  3. Triple bonds

  • Freedom of rotation around single bonds allows for a variety of molecular shapes.

  • Hydrocarbons: Can exist as:

  • Unbranched chains

  • Branched chains

  • Rings

Isomers

• Definition: Compounds with the same molecular formulas but different structures and properties.

• Key Types of Isomers:

  • Structural Isomers: Differ in the covalent arrangement of atoms.

  • Example: Ethanol

    • Formula: C₂H₆O

  • Geometric Isomers (cis-trans): Identical covalent bonds arranged differently in space.

  • Examples:

    • cis-2-butene,

    • trans-2-butene

  • Enantiomers: Mirror images of each other, cannot be superimposed.

Functional Groups

Introduction

• Functional groups replace hydrogens in hydrocarbons, altering the molecule's characteristics.

• Hydrophobic Interactions: Hydrocarbons lack distinct charged regions, are insoluble in water, and tend to group together.

• Polar and ionic functional groups attract water (hydrophilic).

Table 3-1: Some Biologically Important Functional Groups

1. Hydroxyl

   • Structure: R-OH

   • Characteristics: Polar due to electronegative oxygen.

   • Class of Compound: Alcohols.

2. Carbonyl

   • Structure: R-C=O

   • Aldehydes: Carbon is bonded to at least one hydrogen.

   • Ketones: Carbon is bonded to two other carbons.

3. Carboxyl

   • Structure: R-C(=O)OH

   • Characteristics: Weakly acidic; can release H+.

   • Example: Acetic acid (carboxylic acid).

4. Amino

   • Structure: R-NH₂

   • Characteristics: Weakly basic; can accept H+.

   • Example: Amino acids.

5. Phosphate

   • Structure: R-O-P(=O)(OH)₂

   • Characteristics: Weakly acidic; can release H+.

   • Example: Organic phosphates (ATP).

6. Sulfhydryl

   • Structure: R-SH

   • Characteristics: Important in stabilizing protein structures (disulfide bridges).

Functional Groups Summary

• Each functional group has distinctive properties and functions, influencing biological activities in macromolecules such as proteins and carbohydrates.

Polymers

• Definition: Large macromolecules formed by linking monomers.

• Monomers in Proteins:

  • 20 amino acids serve as building blocks for proteins.

• Reactions:

  • Hydrolysis: Breaks down polymers into monomers by adding water.

  • Condensation: Combines monomers by removing a molecule of water, forming covalent bonds.

Carbohydrates

• Composition: Contain carbon, hydrogen, and oxygen in a ratio of approximately 1:2:1, empirical formula: (CH₂O)ⁿ.

• Types:

  • Monosaccharides (one sugar unit)

  • Disaccharides (two sugar units)

  • Polysaccharides (many sugar units)

Monosaccharides

• Simple sugars with 3-7 carbon atoms.

• Common example:

  • Glucose (C₆H₁₂O₆): Most abundant monosaccharide, primary energy source in cells.

Disaccharides

• Formed by two monosaccharide rings joined by a glycosidic linkage.

• Common examples include:

  1. Maltose: 2 α-glucose units

  2. Sucrose: 1 glucose + 1 fructose

  3. Lactose: 1 glucose + 1 galactose

Polysaccharides

• Definition: Macromolecules of repeating simple sugars, typically glucose.

• Common types include:

  1. Starches: Energy storage in plants (consisting of amylose and amylopectin).

  2. Glycogen: Energy storage in animals, more branched than starch.

  3. Cellulose: Structural polysaccharide in plant cell walls; indigestible for humans.

Modified Carbohydrates

• Sugars with unusual functional groups:

  • Galactosamine and glucosamine are important for cartilage structure.

  • Chitin: Found in arthropod exoskeletons and fungal cell walls.

  • Glycosaminoglycans (GAGs): Components of proteoglycans on cell surfaces.

Lipids

• Definition: Compounds soluble in nonpolar solvents; generally insoluble in water.

• Composition: Primarily made of carbon and hydrogen; few oxygen-containing functional groups.

• Major Types:

  1. Fats

  2. Phospholipids

  3. Carotenoids

  4. Steroids

  5. Waxes

Neutral Fats

• Triacylglycerols (Triglycerides): Most abundant lipids, formed from glycerol and three fatty acids.

  • Glycerol: A three-carbon alcohol, bonded to three fatty acids by ester linkages.

• Fatty Acids: Long hydrocarbon chains with a carboxyl group (–COOH) at one end.

Saturated and Unsaturated Fatty Acids

• Saturated Fatty Acids:

  • Maximum number of hydrogen atoms, solid at room temperature.

• Unsaturated Fatty Acids:

  • Contains one (monounsaturated) or more (polyunsaturated) double bonds, liquid at room temperature.

  • Produces a bend in the chain, affecting physical properties and biological roles.

Trans Fats

• Formed through hydrogenation of unsaturated fats, leading to a solid configuration that increases cardiovascular disease risk.

Phospholipids

• Amphipathic lipids: Have a hydrophilic head and hydrophobic tail, critical in forming cell membranes.

Carotenoids

• Plant pigments, yellow and orange, function in photosynthesis.

• Converted to vitamin A in animals, essential for vision.

Steroids

• Composed of carbon in four fused ring structures.

• Examples include cholesterol and reproductive hormones.

Proteins

• Definition: Macromolecules composed of amino acids with diverse functions.

Major Classes of Proteins

• Enzymes: Catalyze chemical reactions (e.g., amylase).

• Structural Proteins: Provide support (e.g., collagen).

• Storage Proteins: Store amino acids (e.g., ovalbumin).

• Transport Proteins: Move substances across membranes (e.g., hemoglobin).

• Regulatory Proteins: Control cell activities (e.g., hormones).

• Motile Proteins: Facilitate movement (e.g., actin).

• Protective Proteins: Defend against pathogens (e.g., antibodies).

Amino Acids

• Basic building blocks of proteins, containing amino and carboxyl groups.

• Exist mainly as dipolar ions at physiological pH.

• Twenty Amino Acids: Grouped by side-chain properties: - Nonpolar (hydrophobic), Polar (hydrophilic), Acidic (carboxyl groups), Basic (accept protons).

Peptide Bonds

• Formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another, link amino acids in polypeptides.

• Polypeptide: A chain of amino acids linked by peptide bonds.

Protein Structure

• Four Levels of Organization:

  1. Primary Structure: Sequence of amino acids.

  2. Secondary Structure: Alpha helices and beta sheets formed by hydrogen bonding.

  3. Tertiary Structure: Overall 3D shape from side-chain interactions.

  4. Quaternary Structure: Complex of multiple polypeptides.

Protein Folding

• Spontaneous in vitro; assisted by molecular chaperones in vivo.

• Misfolding can result in diseases (e.g., Alzheimer's, sickle cell anemia).

Nucleic Acids

• Polymers of nucleotides; transmit hereditary information.

• DNA: Double helix structure, stores genetic information.

• RNA: Single-stranded, vital in protein synthesis.

Components of Nucleotides

1. Five-carbon sugar (deoxyribose or ribose).

2. One or more phosphate groups.

3. Nitrogenous base (purines or pyrimidines).

   • DNA Bases: Adenine, Guanine, Cytosine, Thymine

   • RNA Bases: Adenine, Guanine, Cytosine, Uracil

Important Nucleotides in Energy Transfer

• ATP: Primary energy carrier in cells.

• GTP: Involved in energy transfer.

• NAD+: Key in oxidation-reduction reactions in cells.

References

• Eldra P. Solomon, Charles E. Martin, Diana W. Martin, Linda R. Berg: Biology, Eleventh Edition Student Edition ISBN: 978-1-337-39293-8

• Cengage Learning, Inc. https://www.cengage.com/ except if otherwise stated.