Lecture 2: Amino Acids - Structure, Classification, and Ionization Properties

Comprehensive vocabulary flashcards covering the structure, stereochemistry, classification, specialized derivatives, and acid-base ionization states of amino acids.

Amino Acid General Structure

A molecular structure consisting of an $\alpha$-carbon bonded to four components: a hydrogen atom, an amino group, a carboxylic acid group, and a variable side chain ($R$ group).

Zwitterion

The dipolar ionic form of an amino acid that dominates at neutral $pH$ ($pH\,7$) where the amino group is protonated and the carboxylic group is unprotonated, yielding a net charge of $0$ at the isoelectric point.

Chiral Center in Amino Acids

The asymmetric $\alpha$-carbon bonded to four different chemical groups, a property shared by all standard amino acids except glycine.

Glycine (Gly, G)

The smallest non-polar amino acid whose side chain consists solely of one single hydrogen atom, allowing it to fit into tight structural niches.

Branched-Chain Amino Acids (BCAAs)

A subcategory of hydrophobic non-polar amino acids whose side chains contain branches to increase hydrophobicity; includes Valine (Val, V), Leucine (Leu, L), and Isoleucine (Ile, I).

Alanine (Ala, A)

A non-polar amino acid with a saturated aliphatic side chain that clusters away from water to stabilize 3D protein structure, notable for not containing side chain branches.

Proline (Pro, P)

A non-polar amino acid characterized by a distinctive cyclic structure where its $3$-carbon side chain bonds covalently to the $\alpha$-amino nitrogen.

Aromatic Non-Polar Amino Acids

Hydrophobic amino acids containing an aromatic ring in their side chains, represented by Phenylalanine (Phe, F) and Tryptophan (Trp, W).

Methionine (Met, M)

A non-polar sulfur-containing amino acid ($-CH_2-S-CH_3$) that acts as the initial amino acid in eukaryotic protein synthesis.

Hydroxyl-Containing Polar Amino Acids

Uncharged polar amino acids bearing hydroxyl ($-OH$) groups that confer hydrophilic character; consists of Serine (Ser, S), Threonine (Thr, T), and Tyrosine (Tyr, Y).

Asparagine (Asn, N)

An uncharged polar amino acid that is the amide derivative of aspartic acid; highly polar, frequently found on protein surfaces, and involved in protein folding, ligand binding, and enzyme active sites.

Glutamine (Gln, Q)

The largest polar uncharged amino acid, representing the amide derivative of glutamic acid, which participates in protein structure stabilization and acts as a nitrogen donor.

Cysteine (Cys, C)

An uncharged polar amino acid carrying a sulfhydryl/thiol ($-SH$) group capable of forming covalent disulfide bonds upon oxidation.

Cystine

A covalently linked dimer formed by the oxidation of two cysteine residues via a disulfide bond.

Positively Charged Amino Acids (Basic Side Chains)

Hydrophilic amino acids containing a nitrogenous base side chain with one or more nitrogen atoms; includes Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).

Negatively Charged Amino Acids (Acidic Side Chains)

Dicarboxylic polar amino acids carrying acidic, negatively charged side chains; includes Aspartate (Asp, D) and Glutamate (Glu, E).

Monosodium Glutamate (MSG)

A common flavor enhancer compound derived from the acidic amino acid glutamate.

$N$-Formylmethionine

A translationally incorporated non-standard amino acid that serves as the initial amino acid in bacterial protein synthesis.

Selenocysteine

A translationally incorporated amino acid formed from serine that contains a selenium atom in place of cysteine's sulfur atom.

Pyrrolysine

A translationally incorporated modified form of lysine found naturally in archaebacteria.

Post-Translational Modifications (Amino Acids)

Enzymatic alterations of amino acid residues after protein synthesis, including 4-hydroxyproline, 5-hydroxylysine, phosphoserine, and phosphotyrosine.

Ionizable Groups of Amino Acids

Functional groups capable of gaining or losing protons; non-polar and uncharged polar amino acids possess two ($\alpha$-carboxyl and $\alpha$-amino), while those with ionizable side chains (Lys, Arg, His, Asp, Glu) possess three.

Cationic Form (Low pH)

The fully protonated state assumed by all ionizable groups of an amino acid in an acidic environment of low $pH$.

Anionic Form (High pH)

The deprotonated state assumed by all ionizable groups of an amino acid in a basic environment of high $pH$.