Lecture 5

Key Terms in Organic Chemistry and Biology

• Macromolecule: A large, complex molecule, typically formed by the polymerization of smaller subunits (monomers).

• Hydrocarbon: Organic molecules consisting entirely of carbon and hydrogen.

• Functional groups: Specific groups of atoms within molecules that have characteristic properties and chemical reactivity.

• Hydroxyl (-OH): A functional group consisting of an oxygen atom bonded to a hydrogen atom.

• Carboxyl (-COOH): A functional group composed of a carbonyl and a hydroxyl group attached to the same carbon atom.

• Carbonyl (C=O): A functional group with a carbon atom double-bonded to an oxygen atom.

• Amino (-NH2): A functional group containing a nitrogen atom bonded to two hydrogen atoms.

• Methyl (-CH3): A functional group consisting of a carbon atom bonded to three hydrogen atoms.

• Sulfhydryl (-SH): A functional group containing a sulfur atom bonded to a hydrogen atom.

• Phosphate (-PO42-): A functional group containing a phosphorus atom bonded to four oxygen atoms.

• Sulfate: A functional group containing a sulfur atom surrounded by four oxygen atoms.

• Polymer: A large molecule made up of repeating subunits (monomers).

• Monomer: A small molecule that can join with other similar molecules to form a polymer.

• Dehydration reaction: A chemical reaction in which two molecules are covalently bonded to each other with the removal of a water molecule.

• Hydrolysis reaction: A chemical reaction that breaks bonds between two molecules by the addition of water.

Chemistry of Carbon and Organic Molecules

Properties of Carbon and Its Role in Organic Molecules

Carbon is a unique element that forms the backbone of organic molecules due to its ability to form four covalent bonds, allowing for a diversity of stable structures and molecular complexity.

• Valence Electrons: Carbon has four valence electrons, enabling it to form up to four covalent bonds with other atoms.

• Bonding Diversity: Carbon can form single, double, or triple bonds with other atoms, including other carbon atoms, hydrogen, oxygen, nitrogen, and more.

• Structural Diversity: Carbon skeletons can be straight, branched, or form rings, leading to a wide variety of organic molecules.

• Polarity: The polarity of organic molecules depends on the functional groups attached to the carbon skeleton.

Example: Hydrocarbons (molecules consisting only of carbon and hydrogen) are nonpolar and hydrophobic, while molecules with functional groups like hydroxyl or carboxyl are more polar and hydrophilic.

Hydrocarbons

• Definition: Hydrocarbons are organic molecules composed entirely of carbon and hydrogen.

• Types: Alkanes (single bonds), alkenes (double bonds), and alkynes (triple bonds).

• Properties: Hydrophobic (do not dissolve in water), nonpolar, and can serve as energy sources (e.g., fats).

• Example: Methane (CH4), ethane (C2H6).

Functional Groups in Organic Molecules

Definition and Importance

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactivity of those molecules. They are critical in the structure and function of biological molecules.

• Hydroxyl (-OH): Polar, forms hydrogen bonds, found in alcohols.

• Carbonyl (C=O): Found in aldehydes and ketones, increases reactivity.

• Carboxyl (-COOH): Acts as an acid, found in amino acids and fatty acids.

• Amino (-NH2): Acts as a base, found in amino acids.

• Sulfhydryl (-SH): Forms disulfide bonds, stabilizes protein structure.

• Phosphate (-PO42-): Contributes negative charge, found in nucleic acids and ATP.

• Methyl (-CH3): Nonpolar, affects gene expression.

Example: The difference between estradiol and testosterone is due to the presence of different functional groups, leading to different biological effects.

Table: Major Functional Groups and Their Properties

Functional Group	Structure	Properties	Example Molecule
Hydroxyl	-OH	Polar, forms hydrogen bonds	Ethanol
Carbonyl	C=O	Increases reactivity	Acetone
Carboxyl	-COOH	Acidic, donates H+	Acetic acid
Amino	-NH2	Basic, accepts H+	Glycine
Sulfhydryl	-SH	Forms disulfide bonds	Cysteine
Phosphate	-PO42-	Negative charge, energy transfer	ATP
Methyl	-CH3	Nonpolar, gene regulation	5-methylcytosine

Biological Macromolecules

The Four Classes of Biological Molecules

Living organisms are composed of four major classes of biological macromolecules, each with distinct structures and functions.

• Carbohydrates: Serve as energy sources and structural materials. Monomers are monosaccharides (e.g., glucose).

• Lipids: Hydrophobic molecules including fats, phospholipids, and steroids. Not true polymers.

• Proteins: Polymers of amino acids, perform a wide range of functions including catalysis, structure, and transport.

• Nucleic Acids: Polymers of nucleotides, store and transmit genetic information (DNA, RNA).

Polymers and Monomers

• Polymer: A long molecule consisting of many similar or identical building blocks linked by covalent bonds.

• Monomer: The repeating subunit that serves as the building block of a polymer.

• Examples:

  • Proteins: monomers are amino acids

  • Carbohydrates: monomers are monosaccharides

  • Nucleic acids: monomers are nucleotides

Polymerization Reactions

• Dehydration (Condensation) Reaction: Joins two monomers by removing a water molecule.

• Hydrolysis Reaction: Breaks a bond between monomers by adding a water molecule.

Example Equation:

Dehydration synthesis of two glucose molecules to form maltose:

$C_6H_{12}O_6 + C_6H_{12}O_6 \rightarrow C_{12}H_{22}O_{11} + H_2O$

Hydrolysis is the reverse reaction, breaking maltose into two glucose molecules by adding water.

Types of Covalent Bonds in Macromolecules

• Peptide bonds: Link amino acids in proteins.

• Glycosidic bonds: Link monosaccharides in carbohydrates.

• Phosphodiester bonds: Link nucleotides in nucleic acids.

Summary Table: Macromolecules, Monomers, and Bonds

Macromolecule	Monomer	Covalent Bond	Example
Protein	Amino acid	Peptide bond	Hemoglobin
Carbohydrate	Monosaccharide	Glycosidic bond	Starch
Nucleic Acid	Nucleotide	Phosphodiester bond	DNA
Lipid	Glycerol, fatty acids	Ester bond	Triglyceride

Dehydration and Hydrolysis Reactions

Comparison

• Dehydration Reaction: Builds polymers from monomers, releases water.

• Hydrolysis Reaction: Breaks polymers into monomers, consumes water.

• Dependence on Water: Dehydration removes water; hydrolysis adds water.

Additional info:

• ATP (adenosine triphosphate) is a nucleotide that stores and releases energy for cellular processes. The hydrolysis of ATP to ADP releases energy:

$ATP + H_2O \rightarrow ADP + P_i + \text{energy}$

• Functional groups determine the solubility, reactivity, and biological activity of organic molecules.