Introduction: The Chemistry of Life
Welcome to Organic Chemistry, the study of carbon-containing compounds. This field is the foundation of biochemistry and is essential for understanding the molecules that make life possible. In this lesson, we will explore the simplest organic molecules—hydrocarbons—, the concept of isomers, and the critically important functional groups that define the properties of biomolecules.
Part 1: Hydrocarbons & Isomers
1.1 Hydrocarbons: The Simplest Organic Molecules
Hydrocarbons are organic compounds composed entirely of carbon and hydrogen atoms. They are the backbone of many larger organic molecules. We classify them based on the types of carbon-carbon bonds they contain.
Alkanes: Saturated Hydrocarbons (C-C)
Alkanes are hydrocarbons that contain only single bonds between carbon atoms. They are called saturated because they have the maximum possible number of hydrogen atoms bonded to the carbon skeleton. Their names typically end in "-ane". The general formula is $C_nH_{2n+2}$.
Alkenes: Unsaturated Hydrocarbons (C=C)
Alkenes contain at least one double bond between carbon atoms. They are unsaturated because they have fewer than the maximum number of hydrogen atoms. Their names typically end in "-ene". The double bond is a site of higher reactivity.
Alkynes: Unsaturated Hydrocarbons (C≡C)
Alkynes contain at least one triple bond between carbon atoms. They are also unsaturated and are even more reactive than alkenes. Their names typically end in "-yne".
Diagram: Ethane, Ethene, and Ethyne
1.2 Isomers: Same Formula, Different Structure
Isomers are compounds that have the same molecular formula but different structures and, therefore, different properties. This concept is crucial in organic chemistry because it explains the vast diversity of organic molecules.
Structural Isomers
These isomers differ in the covalent arrangement of their atoms. For example, Butane and Isobutane both have the formula $C_4H_{10}$ but their carbon skeletons are arranged differently.
Geometric Isomers (Cis-Trans)
These isomers have the same covalent partnerships but differ in their spatial arrangement around a double bond, which does not permit free rotation.
Enantiomers (Stereoisomers)
Enantiomers are isomers that are non-superimposable mirror images of each other, like left and right hands. This occurs when a carbon atom is bonded to four different groups. This carbon is called a chiral center. Enantiomers have nearly identical physical and chemical properties but can have vastly different biological effects.
Diagram: Enantiomers (Mirror Images)
Part 2: Functional Groups
2.1 The Components of Organic Molecules
The properties of an organic molecule depend not only on its carbon skeleton but also on the molecular components attached to it. Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules.
| Functional Group | Structure | Properties & Role in Biomolecules |
|---|---|---|
| Hydroxyl (-OH) | R-O-H | Forms alcohols. Is polar, making molecules water-soluble. Found in carbohydrates. |
| Carbonyl (C=O) | R-CO-R' (Ketone) R-CO-H (Aldehyde) |
A key feature of carbohydrates (sugars). Ketones are within the skeleton, Aldehydes are at the end. |
| Carboxyl (-COOH) | R-COOH | Forms carboxylic acids. Acts as an acid (donates H+). Found in amino acids and fatty acids. |
| Amino (-NH₂) | R-NH₂ | Forms amines. Acts as a base (accepts H+). A key component of all amino acids. |
| Sulfhydryl (-SH) | R-SH | Forms thiols. Two sulfhydryl groups can react to form a "disulfide bridge," which stabilizes protein structure. |
| Phosphate (-OPO₃²⁻) | R-OPO₃²⁻ | Contributes negative charge. Molecules with phosphate groups have potential to react with water, releasing energy. Found in ATP and DNA/RNA. |
Part 3: Functional Groups in Biomolecules
3.1 Carbohydrates & Lipids
Carbohydrates (sugars) are characterized by the presence of a carbonyl group and multiple hydroxyl groups. Their high number of polar hydroxyl groups makes them hydrophilic. Lipids (fats) are largely hydrocarbons. A fatty acid has a long nonpolar hydrocarbon tail and a polar carboxyl group head.
3.2 Proteins (Amino Acids)
Proteins are polymers of amino acids. Each amino acid has a central chiral carbon, an amino group, a carboxyl group, a hydrogen, and a variable R-group. The amino and carboxyl groups are essential for forming peptide bonds, which link amino acids together in a chain.