Proteins and Amino Acids

Comprehensive vocabulary flashcards covering the structure, classification, chemical properties, reactions, and acid-base titration characteristics of amino acids and proteins.

Proteins

Abundant biological macromolecules that are polymers of amino acids whose sequence is dictated by the nucleotide sequence of chromosomal DNA (e.g., AUG encoding Methionine).

$\alpha$-Carbon

The central carbon atom of an amino acid covalently bonded to four distinct groups (a carboxyl group, an amino group, an R group, and a hydrogen atom) in all standard amino acids except glycine.

L-Isomers (Amino Acids)

The predominant stereoisomeric configuration adopted by amino acid residues in biological systems due to their greater thermodynamic stability compared to D-isomers.

Nonpolar, Aliphatic R Groups

Hydrophobic amino acid side chains (glycine, alanine, proline, valine, leucine, isoleucine, and methionine) that cluster within proteins to stabilize structure via hydrophobic interactions.

Aromatic R Groups

Relatively nonpolar amino acid side chains (phenylalanine, tyrosine, and tryptophan) that stabilize protein structures through hydrophobic interactions and absorb ultraviolet light at $280\,\text{nm}$.

Cystine

A dimeric amino acid unit formed by the reversible oxidation of two cysteine molecules joined by a covalent disulfide bond, accompanied by the release of $2\text{H}^+$ and $2e^-$.

Histidine

A basic amino acid possessing an ionizable imidazole side chain with a $pK_a$ near neutrality ($6.1$), allowing it to serve as a biological buffer and catalytic residue in enzymes.

Positively Charged R Groups

Hydrophilic, basic amino acids that carry a net positive charge at $\text{pH } 7$, comprising lysine, arginine, and histidine.

Negatively Charged R Groups

Hydrophilic, acidic amino acids that carry a net negative charge at $\text{pH } 7$, comprising aspartate and glutamate.

4-Hydroxyproline and 5-Hydroxylysine

Uncommon, post-translationally modified amino acids found as essential structural components in collagen.

$\gamma$-Carboxyglutamate

An uncommon amino acid residue containing an additional carboxyl group introduced on its side chain, found in blood-clotting proteins.

Desmosine

A complex cross-linked amino acid structure derived from four lysine residues found in elastin, relevant to the vasoconstriction and vasodilation of blood vessels.

Essential Amino Acids

Ten amino acids that cannot be synthesized by the body and must be supplied through diet: phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histidine, arginine, lysine, and leucine (PVTTIMHALL).

Non-essential Amino Acids

Amino acids that can be synthesized endogenously by the body, including glycine, alanine, proline, tyrosine, asparagine, cysteine, glutamine, serine, aspartate, and glutamate.

Glucogenic Amino Acids

Amino acids whose degraded carbon skeletons can be converted into glucose or TCA cycle intermediates (e.g., serine, threonine, glycine, alanine, and valine).

Ketogenic Amino Acids

Amino acids whose carbon skeletons are catabolized exclusively to acetoacetyl-CoA or acetyl-CoA (ketone body precursors), strictly consisting of leucine and lysine.

Zwitterion

A dipolar ionic form of an amino acid having separate positively ($-\text{NH}_3^+$) and negatively ($-\text{COO}^-$) charged groups, giving a net charge of zero in neutral aqueous solutions.

Ampholytes

Compounds, such as amino acids, that possess dual acid-base properties and can act as either proton donors or proton acceptors depending on the surrounding $\text{pH}$.

Ninhydrin Reaction

A colorimetric test where free amino groups react with ninhydrin to produce a purple-colored solution; proline cannot yield this purple color because it lacks a primary free amino group.

Schiff Base Formation

A chemical reaction in which the primary amino group of an amino acid condenses with an aldehyde (such as benzaldehyde) to form an imine linkage ($-\text{N=CH}-$) with the release of water.

Van Slyke Reaction

A diagnostic reaction where primary amino groups of amino acids react with nitrous acid ($\text{HNO}_2$) to produce stoichiometric elemental nitrogen gas ($\text{N}_2$).

Sanger's Reagent

2,4-Dinitrofluorobenzene, a chemical compound that reacts with the unprotonated amino group of an amino acid or peptide to yield a yellow dinitrophenyl precipitate.

Isoelectric Point ($pI$)

The specific $\text{pH}$ at which an amino acid molecule carries no net electrical charge; for simple monoamino monocarboxylic acids, it is calculated as $\frac{pK_1 + pK_2}{2}$.

Titration Curve of Glycine

A titration plot showing two distinct buffering zones ($pK_1$ for the carboxyl group and $pK_2$ for the amino group) and an isoelectric point ($pI$) near neutral $\text{pH}$.

Titration Curve of Glutamate

A titration plot featuring three buffering regions ($pK_1$, $pK_2$, and $pK_3$) with an acidic isoelectric point ($pI$) calculated from the average of the two lowest $pK_a$ values.

Titration Curve of Lysine

A titration plot for a basic amino acid with three ionizable groups, whose isoelectric point ($pI$) is calculated in the basic range as $\frac{8.95 + 10.5}{2} = 9.7$.