Ch. 10 - Nitrogen and Phosphorus Containing Compounds

4% of MCAT Organic content

What groups are attached to the α-carbon of an amino acid?

• Amino group, carboxyl group, hydrogen atom, and R group.

• Chiral stereocenter in all amino acids except glycine.

What is the stereochemistry of amino acids in eukaryotes?

• All are L-amino acids.

• All have (S) stereochemistry except cysteine, which is (R).

What does it mean that amino acids are amphoteric?

• They can act as acids or bases.

• Acidic properties from the carboxylic acid group.

• Basic properties from the amino group.

What is a zwitterion?

• A dipolar ion where the amino acid has both a positive and negative charge.

• Common in neutral solutions.

How are amino acids classified based on their R groups?

1. Nonpolar nonaromatic: Alanine, valine, leucine, isoleucine, glycine, proline, methionine.

2. Aromatic: Tryptophan, phenylalanine, tyrosine.

3. Polar: Serine, threonine, asparagine, glutamine, cysteine.

4. Negatively charged (acidic): Aspartic acid, glutamic acid.

5. Positively charged (basic): Arginine, lysine, histidine.

Which amino acids are hydrophobic or hydrophilic?

• Hydrophobic: Nonpolar nonaromatic and aromatic amino acids; found in protein interiors.

• Hydrophilic: Polar, acidic, and basic amino acids; found on protein surfaces, forming hydrogen bonds.

What is the nature of peptide bonds?

• Formed by condensation reactions.

• Cleaved hydrolytically by strong acid or base.

• Resonance restricts motion around the CN bond, giving partial double-bond character.

What are polypeptides and proteins?

• Polypeptides: Chains of amino acids linked by peptide bonds.

• Proteins: Large, folded, functional polypeptides.

What is the Strecker synthesis?

1. Mix aldehyde with ammonium chloride (NH₄Cl) and potassium cyanide (KCN).

2. Ammonia attacks the carbonyl carbon, forming an imine.

3. Cyanide attacks the imine, forming an aminonitrile.

4. Hydrolyze the aminonitrile with two water equivalents to produce an amino acid.

What is the Gabriel synthesis?

1. Phthalimide attacks diethyl bromomalonate, forming a phthalimidomalonic ester.

2. Ester attacks an alkyl halide, adding an alkyl group.

3. Hydrolyze to form phthalic acid and convert esters into carboxylic acids.

4. Decarboxylate one carboxylic acid, yielding an amino acid.

What is inorganic phosphate (Pi), and where is it found?

• Buffered mixture of HPO₄²⁻ and H₂PO₄⁻.

• Found in DNA backbone (phosphodiester bonds) and nucleotide triphosphates (e.g., ATP, GTP).

What is pyrophosphate (PPi), and what happens to it?

• Released during phosphodiester bond formation.

• Hydrolyzed into two inorganic phosphates.

Why are phosphate bonds high energy?

• Large negative charges in adjacent phosphate groups.

• Resonance stabilization of phosphates.

What are organic phosphates, and why is phosphoric acid a good buffer?

• Organic phosphates: Carbon-containing molecules with phosphate groups (e.g., ATP, GTP).

• Buffering ability: Phosphoric acid has three hydrogens, each with a unique pKa, allowing buffering over a wide pH range.