MCAT Organic Chemistry - Nitrogen- and Phosphorus-Containing Compounds

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Amino acids

contain an amino group and a carboxyl group attached to a single carbon atom; other two substituents of the α-carbon are a hydrogen atom and a side chain; stereogenic center EXCEPT glycine; L-isomers (S configuration EXCEPT cysteine)

R group

side chain esp. of an amino acid

Glycine

simplest amino acid; achiral; R group is a hydrogen atom

cysteine

R group is thiol (-SH); covalent bonding, only (R) configuration amino acid

amphoteric

act as both acids and bases

zwitterion

dipolar ion

nonpolar nonaromatic amino acids

tend to have side chains that are saturated hydrocarbons: alanine, valine, leucine, and isoleucine

also include glycine, proline (which is cyclic, with a secondary amine), and methionine (which contains sulfur)

Aromatic amino acids

tryptophan, phenylalanine, and tyrosine

Nonpolar amino acids

hydrophobic and tend to be sequestered in the interior of proteins

Polar amino acidS

tend to have terminal groups containing oxygen, nitrogen, or sulfur: serine, threonine, asparagine, glutamine, and cysteine

Negatively charged (acidic) amino acids

terminal carboxylate anions

aspartic acid and glutamic acid

positively charged (basic) amino acids

protonated amino group in their R groups

arginine, lysine, and histidine

peptide bonds

condensation reactions of amino acids

polypeptides

molecules formed from amino acids bonded by peptide bonds

proteins

Biomolecule consisting of folded chains of amino acid residues

Resonance in the Peptide Bond

partial double-bond character between the nitrogen atom and the carbonyl carbon; limits rotation about the C―N bond, which adds to the rigidity and stability of the backbone

Strecker synthesis

aldehyde, ammonium chloride (NH4Cl), and potassium cyanide (KCN) → aminonitrile → amino acid (racemic)

Gabriel (malonic-ester) synthesis

potassium phthalimide + diethyl bromomalonate → phthalimidomalonic ester + bromoalkane → hydrolysed with heat → dicarboxylic acid with an amine on the α-carbon → decarboxylated through the addition of acid and heat → complete amino acid (racemic)

Phosphoric acid / phosphate group / inorganic phosphate (Pi)

forms the high-energy bonds that carry energy in adenosine triphosphate (ATP); three acidic hydrogens when fully protonated; both hydrogen phosphate and dihydrogen phosphate in cell; experience a large amount of repulsion from each other because they are negatively charged

pKas: 2.15, 7.20, 12.32

phosphodiester bonds

linking the phosphate groups and sugar moieties of the nucleotides into nucleic acids

pyrophosphate (P₂O₇^4-) (PP_i)

ester dimer of phosphate released by nucleotide as it adds to nucleic acidc chain; unstable in aqueous solution and is hydrolyzed to form two molecules of inorganic phosphate that can be recycled

organic phosphates

Nucleotides, due to the presence of the phosphate group bonded to a carbon-containing molecule