Carboxylic Acids

Structure and Properties

Carboxylic acids are organic compounds containing a carbonyl group (C=O) bonded to a hydroxyl group (–OH). They are more oxidized than aldehydes and ketones and are key functional groups in biochemistry.

• Intermolecular forces: Carboxylic acids form hydrogen bonds, acting as both donors and acceptors.

• Solubility: Usually water-soluble unless the carboxyl group is a small percentage of the molecule's mass (e.g., fatty acids).

• Acidity: Carboxylic acids are weak acids, with typical pKa values around 3-4. They can donate a proton to water.

Carboxylate Salts

Carboxylate salts are formed by the neutralization of carboxylic acids with metal hydroxides.

• Structure: Ionic species, more water-soluble than their parent acids.

• Example: Soap is a carboxylate salt of fatty acids.

Reactions

• Neutralization:

• Esterification:

• Amide formation:

Carboxylic Acids in Proteins

Acidic amino acids (e.g., glutamate) contain carboxylic acid groups, which can be protonated or deprotonated depending on pH.

• Speciation:

Esters

Structure and Properties

Esters are derived from carboxylic acids and alcohols, containing a carbonyl group bonded to an oxygen atom.

• Intermolecular forces: Dipole-dipole interactions; only hydrogen bond acceptors.

• Solubility: Can hydrogen bond with water, but less soluble than carboxylate salts.

• Volatility: More volatile and lower boiling point than carboxylic acids.

Formation and Hydrolysis

• Esterification:

• Hydrolysis:

• Saponification (base hydrolysis):

Example: Triacylglycerols (TAGs)

TAGs are esters formed from fatty acids and glycerol, important in biochemistry.

• Hydrolysis: Produces fatty acids and glycerol.

Amines

Structure and Classification

Amines are derivatives of ammonia (NH3), classified by the number of carbon groups attached to the nitrogen.

• Primary (1°) amine: One carbon attached

• Secondary (2°) amine: Two carbons attached

• Tertiary (3°) amine: Three carbons attached

• Quaternary (4°) ammonium: Four carbons, positive charge

Properties

• Intermolecular forces: 1° and 2° amines can hydrogen bond; 3° amines have dipole-dipole interactions.

• Solubility: Usually water-soluble unless large hydrophobic groups are present.

• Odor: Many amines have strong, unpleasant odors.

Amines as Bases

Amines can accept protons, acting as weak bases.

• Reaction with acids: Forms ammonium salts, which are more water-soluble.

• Reaction with water: Forms ammonium ions.

Examples: Alkaloids and Drugs

• Alkaloids: Plant-derived amines, often pharmacologically active (e.g., caffeine, nicotine).

• Drugs: Many drugs are amine salts to increase solubility (e.g., fluoxetine hydrochloride).

Amides

Structure and Formation

Amides are formed from the reaction of carboxylic acids and amines, containing a carbonyl group bonded to nitrogen.

• Classification: Primary, secondary, and tertiary amides, depending on the number of carbons attached to nitrogen.

• Formation:

Properties

• Intermolecular forces: 1° and 2° amides can hydrogen bond; 3° amides have dipole-dipole interactions.

• Solubility: Usually water-soluble unless large hydrophobic groups are present.

• Basicity: Amides are not basic; the nitrogen lone pair is attracted to the carbonyl carbon.

Amides in Proteins: Peptide Bonds

Proteins are synthesized by linking amino acids via amide bonds, called peptide bonds.

• Hydrolysis: Amides can be hydrolyzed under acidic or basic conditions to form amine salts or carboxylate salts.

Thiols and Thioesters

Thiols

Thiols are similar to alcohols, but contain sulfur instead of oxygen.

• Properties: Dipole-dipole interactions, do not form hydrogen bonds, less polar than alcohols.

• Odor: Characteristic "skunky" smell; used as odorant in natural gas.

• Reactivity: More reactive than alcohols; can be oxidized to form disulfides.

Disulfide Formation

• Oxidation: Two thiols can be oxidized to form a disulfide bond.

• Reversibility: Disulfide bonds can be reduced back to thiols.

Thioesters

Thioesters are similar to esters, but contain sulfur instead of oxygen. They are important in metabolism (e.g., acetyl-CoA).

• Formation: Carboxylic acid + thiol.

• Energy: Thioesters are higher energy than esters when hydrolyzed.

Phosphate Compounds

Phosphoesters and Phosphoanhydrides

Phosphate compounds are essential in biochemistry, forming the backbone of DNA and acting as energy carriers.

• Phosphoester: C—O—P bond, formed from reaction of phosphate with alcohol.

• Phosphoanhydride: P—O—P bond, formed from reaction of two phosphates by elimination of water.

Phosphate Backbone of DNA

• Nucleotides: Contain phosphate esters; nucleic acids are built from nucleotides.

• Phosphate diesters: Link nucleic acid chains.

ATP: Adenosine Triphosphate

ATP contains phosphoanhydride bonds, which release energy when broken. ATP is the primary energy carrier in cells.

• Energy: Negative charges on phosphate oxygens create bond strain, making hydrolysis energetically favorable.

Phosphorylation Reactions

Phosphorylation is the transfer of a phosphate group from one molecule to another, often using ATP.

• Example: In glycolysis, a phosphate group is transferred from ATP to glucose.

• Equation:

Summary Table: Functional Groups and Properties