Comprehensive Study Notes on Amines, Amides, Amino Acids, and Carbonyl Reactions

Ammonia serves as a foundational example of an amine. It exists as a gas ( $NH_3$ ) but is highly soluble in water.
Commercial Ammonia: The ammonia purchased in the cleaning aisle of stores like Safeway is not pure ammonia; it is an aqueous solution of ammonia gas dissolved in water. It is a basic substance, making it an effective cleaning agent for specific applications.
Methylamine ( $CH_3NH_2$ ): This compound is also a gas at room temperature.
Breaking Bad Discrepancy: The television series Breaking Bad features a plot point where characters (notably Todd, who shoots a child on a bicycle) steal methylamine from a railroad car. The show depicts methylamine as a liquid to facilitate the scene, but in reality, it is a gas, illustrating that the show's depiction is fictional.

Amines act as bases, meaning they can accept protons ( $H^+$ ) from acids.
Reaction with Hydrochloric Acid ( $HCl$ ): - When an amine reacts with aqueous hydrochloric acid ( $HCl_{(aq)}$ ), the lone pair of electrons on the nitrogen atom is used to form a bond with a hydrogen ion from the acid. - Example: Reacting dimethylamine ( $(CH_3)_2NH$ ) with $HCl$ results in the formation of a salt. - The nitrogen gains a positive charge, while the chlorine remains as a negatively charged ion ( $Cl^-$ ).
Nomenclature of Amine Salts: When an amine picks up a hydrogen atom from an acid, it is no longer classified as an amine in naming; it becomes an ammonium. - The product of dimethylamine and hydrochloric acid is named dimethylammonium chloride.
Reaction with Water: - Ammonia ( $NH_3$ ) can react with water ( $H_2O$ ), where water acts as an acid by donating a hydrogen ion. - The reaction is: $NH_3 + H_2O \rightleftharpoons NH_4^+ + OH^-$ . - The resulting compound is ammonium hydroxide ( $NH_4OH$ ). - In this compound, the nitrogen has no substituents other than hydrogens, making it a "plain old" ammonium ion.

Aqueous Reaction Vessels: Humans are described as aqueous reaction vessels because biological reactions occur in water-based solutions. Solubility is critical for molecules to interact and react.
Solubility Shift: Amines are molecules of moderate polarity (nitrogen is near oxygen on the periodic table). For instance, an amine with four carbons and one nitrogen has some water solubility.
Ionic Transformation: When an amine reacts with an acid to become an ammonium salt, it becomes an ionic compound. - Rule of Solubility: Ions/salts are significantly more water-soluble than neutral polar molecules. As noted, "The ocean is salty" because water molecules are highly attracted to charged ions.
Biological Applications: - Blood testing involves measuring dissolved substances like calcium, sodium, potassium, and triglycerides. - For these to be in the blood, they must be water-soluble or associated with a water-soluble carrier molecule. - Micelles: Spherical structures (like those formed by soap) can trap non-polar substances (like chicken grease) and use a polar exterior to pull them into solution.
Structural Integrity: While solubility is essential for reactions, some structures must remain insoluble, such as bones, to prevent the human body from becoming soft like an octopus.

Amines are classified based on the number of organic groups (R-groups) attached to the nitrogen atom: - Primary ( $1^{\circ}$ ) Amine: The nitrogen is attached to two hydrogens, one lone pair, and one R-group (a carbon-based group). - Secondary ( $2^{\circ}$ ) Amine: The nitrogen is attached to one hydrogen and two R-groups. - Tertiary ( $3^{\circ}$ ) Amine: The nitrogen is attached to three R-groups and has no hydrogens bonded directly to it.
Ammonia ( $NH_3$ ) is considered the starting point for these classifications.

Amide Definition: An amide is a functional group featuring a nitrogen atom attached to a carbonyl group ( $C=O$ ).
Basicity: Unlike amines, amides are not basic under biological conditions. While a very strong acid could potentially force a proton onto an amide, they do not form salts like amines do in the body.
Classification: Amides also have primary, secondary, and tertiary forms depending on the number of substituents on the nitrogen, though the lecturer notes this is less critical than amine classification.
Biological and Industrial Significance: - Proteins are polymers composed of many amides. - Nylon: An example of a manufactured (synthetic) amide. - Textiles: - Plants (Cotton, Linen): These are carbohydrates/sugars. - Animals (Wool, Silk): These are proteins made of amides/amino acids.

Definition: An amino acid contains both an amine group (often called an "amino" group in this context) and a carboxylic acid group on the same molecule.
The Zwitterion: Because the molecule contains both a base (the amine) and an acid (the carboxylic acid), an internal acid-base reaction occurs. - The carboxylic acid donates a hydrogen ion ( $H^+$ ) to the amine group. - This results in a molecule with a positive charge on the nitrogen ( $NH_3^+$ ) and a negative charge on the carboxylate ( $COO^-$ ). - This dual-charged, overall neutral molecule is called a zwitterion (from the German word for "hybrid" or "hermaphrodite").
Nomenclature and Cheat Sheets: - Amino acids have common names (e.g., Glycine, Leucine, Tyrosine). - They are abbreviated with three letters (e.g., Gly, Leu) and single letters (e.g., G, L). - Tyrosine (Y): A mnemonic for remembering that Tyrosine is "Y" is the question: "Why the hell did they name Tyrosine y?"

The Hydronium Ion: In aqueous acid solutions, the proton ( $H^+$ ) associates with water to form hydronium ( $H_3O^+$ ).
Hydrates: When an aldehyde or ketone is placed in water with an acid catalyst, it forms a hydrate (a molecule with two hydroxyl groups on the same carbon). - This exists in an equilibrium reaction.
Acetals and Hemiacetals: - If an aldehyde reacts with an alcohol (e.g., methanol, $CH_3OH$ ) and an acid catalyst, it forms an acetal. - The intermediate stage, where the molecule has one alcohol group ( $OH$ ) and one ether-like group ( $OR$ ) on the same carbon, is called a hemiacetal. - Cyclification: If an alcohol contains two hydroxyl ( $OH$ ) groups, it can react with a carbonyl to put both oxygen atoms onto the same compound.

Question/Topic: Identifying the product of an amine reacting with an acid. - Speaker Response: The lone pair on the nitrogen forms a bond with the hydrogen from the acid, resulting in a positive charge on the nitrogen (the ammonium ion) and a negative counter-ion (the chloride).
Question/Topic: Why is the solubility of ionic salts important in biochemistry? - Speaker Response: Because the body is an aqueous vessel, and reactions must happen in solution. We need to be able to control what dissolves (like nutrients in blood) and what does not (like bones).