Amino Acids, Functional Groups, and Protein Chemistry

Vocabulary flashcards covering the functional groups, chemical properties, classifications, and structures of amino acids and proteins from the lecture.

Peptide bond

An amide functional group that connects amino acids to each other in a protein.

Thiol

A functional group in which an $SH$ group is connected to an alkane-type or tetrahedral carbon atom, found in the amino acid cysteine.

Cysteine

One of the $20$ amino acids that make up proteins; it contains a thiol functional group in its side chain, is classified as polar neutral, and has the three-letter abbreviation CYS.

Sulfide

An organic functional group in which a sulfur atom is covalently bonded to two tetrahedral carbon atoms, found in the amino acid methionine.

Methionine

A nonpolar amino acid that contains a sulfide functional group in its side chain.

Disulfide

A functional group consisting of two sulfur atoms covalently bonded to each other and in turn covalently bonded to two tetrahedral carbon atoms, helping proteins fold into compact shapes.

Primary amine

An amine in which one of the three covalent bonds of the nitrogen atom is connected to a carbon atom and two bonds are connected to hydrogen atoms.

Secondary amine

An amine in which two of the three covalent bonds of the nitrogen atom are connected to carbon atoms and one bond is connected to a hydrogen atom.

Tertiary amine

An amine in which all three covalent bonds of the nitrogen atom are connected to carbon atoms, preventing it from forming hydrogen bonds with other tertiary amine molecules.

Carboxylate ion

The negatively charged conjugate base formed when a carboxylic acid donates a proton to water; it predominates at physiological pH to increase water solubility.

Palmitic acid

A fatty acid that exists as a hydrophobic, nonpolar carboxylic acid at pH below $5$, and forms an amphipathic carboxylate ion at physiological pH of around $7$.

Amphipathic molecule

A molecule that is intermediate between hydrophobic and hydrophilic, making it soluble in water to some degree (such as a carboxylate ion of a fatty acid).

Quaternary ammonium ion

A positively charged cation formed when an amine accepts a proton, resulting in a nitrogen atom with four covalent bonds.

Alpha amino acid

An amino acid in which the amine functional group and the carboxylic acid functional group are separated by exactly one carbon atom.

Zwitterion

A double ion molecule bearing one positive charge and one negative charge such that it is overall electrically neutral, typically formed by amino acids at physiological pH $7$.

Nonpolar amino acids

A group of $9$ amino acids whose side chains are dominated by nonpolar bonds, such as carbon-carbon and carbon-hydrogen bonds, and include alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, and tryptophan.

Polar acidic amino acids

A subclass of $2$ amino acids containing a carboxylic acid functional group in their side chains, which donates a proton at physiological pH $7$ to exist as an anion.

Polar basic amino acids

A subclass of $3$ amino acids (lysine, arginine, and histidine) that contain amine functional groups in their side chains, which act as Bronsted-Lowry proton acceptors to form cations at physiological pH $7$.

Polar neutral amino acids

A subclass of polar amino acids with a side chain net charge of zero, including serine, threonine, cysteine, tyrosine, asparagine, and glutamine.