Amino Acids, Peptides, and Protein Structure

Vocabulary practice flashcards covering amino acid structures, chemical classifications, acid-base properties, titration behavior, peptide bonds, and levels of protein structure.

Proteinogenic amino acids

The $20$ amino acids that serve as the universal building blocks for proteins across all living organisms.

$\alpha$-Carbon ($\alpha$-carbon)

The central carbon atom of an amino acid directly adjacent to the carboxylic acid group, bonded to an amino group, a hydrogen atom, and a variable side chain ($R$-group).

Zwitterion

A dipolar molecule carrying an internal positive charge and an internal negative charge at distinct positions, resulting in an electrically neutral state overall.

Glycine (Gly, G)

The simplest proteinogenic amino acid, having a single hydrogen atom as its side chain, making it the only achiral amino acid.

Alanine (Ala, A)

An aliphatic amino acid featuring a methyl group ($-\text{CH}_3$) as its side chain, from which most other amino acids are structurally derived.

Proline (Pro, P)

An aliphatic amino acid whose side chain connects to both the $\alpha$-carbon and the backbone nitrogen atom to form a five-membered ring, giving it a unique secondary amine.

Branched-chain amino acids (BCAAs)

A group of aliphatic nonpolar amino acids containing branched alkyl side chains, consisting specifically of valine, leucine, and isoleucine.

Aromatic amino acids

A group of amino acids containing aromatic ring systems in their side chains, comprising phenylalanine, tyrosine, and tryptophan.

Methionine (Met, M)

A nonpolar aliphatic amino acid containing two methylene groups attached to a nonpolar methyl thioether.

Cysteine (Cys, C)

A polar neutral amino acid containing a reactive thiol ($-\text{SH}$) group that can undergo redox reactions to form covalent disulfide bonds.

Histidine (His, H)

An amino acid with an aromatic imidazole ring side chain ($\text{p}K_{\text{a}} \approx 6.0$) that is predominantly neutral and deprotonated at physiological $\text{pH}$ ($7.4$), with fewer than $10\%$ of molecules carrying a positive charge.

Basic amino acids

Positively charged amino acids under physiological conditions that acquire positive charge by accepting protons, predominantly comprising lysine and arginine.

Acidic amino acids

Negatively charged amino acids under physiological conditions that acquire negative charge by losing protons, comprising aspartate and glutamate.

Ionizable amino acids

The seven amino acids whose side chains can exchange protons with the environment to carry an electric charge: arginine, lysine, histidine, tyrosine, cysteine, glutamate, and aspartate.

$$\text{p}K_{\text{a}}$$

The specific $\text{pH}$ at which exactly $50\%$ of a population of ionizable chemical groups is protonated and $50\%$ is deprotonated.

Isoelectric point ($\text{pI}$)

The specific $\text{pH}$ at which the average net electrical charge of a population of amino acid or peptide molecules is exactly zero.

Buffer region

The relatively flat segment of a titration curve spanning $1\,\text{pH}$ unit below to $1\,\text{pH}$ unit above an ionizable group's $\text{p}K_{\text{a}}$, where the group effectively resists changes in $\text{pH}$.

Peptide bond

The covalent amide bond formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another via a condensation reaction, with the accompanying loss of water.

Partial double bond character

The resonance delocalization of nitrogen lone-pair electrons into the carbonyl group of a peptide bond, creating a rigid, planar structure with restricted rotation.

Amino terminus (N-terminus)

The end of a peptide or protein bearing an unlinked, free $\alpha$-amino group, representing the start of a polypeptide chain.

Carboxy terminus (C-terminus)

The end of a peptide or protein bearing an unlinked, free $\alpha$-carboxyl group, representing the end of a polypeptide chain where new residues are added.

Average amino acid residue mass

The standard average molecular weight used to estimate protein size, equal to approximately $110\,\text{Da}$ ($0.11\,\text{kDa}$) per amino acid residue.

Primary protein structure

The linear sequence of amino acid residues in a polypeptide chain linked by covalent peptide bonds, determined directly by genetic code.

Secondary protein structure

Localized, repetitive conformational arrangements of the polypeptide backbone stabilized by hydrogen bonds between backbone amide $\text{N}-\text{H}$ and carbonyl $\text{C}=\text{O}$ groups.

$\alpha$-Helix

A right-handed coiled secondary structure motif in which each backbone $\text{N}-\text{H}$ group forms a hydrogen bond with the backbone $\text{C}=\text{O}$ group of the residue four positions earlier ($i$ to $i+4$), with $3.6$ residues ($5.4\,\text{Å}$) per turn.

$\beta$-Pleated sheet

A secondary structure consisting of laterally aligned $\beta$-strands connected by backbone hydrogen bonds, organized in either parallel or antiparallel arrangements.

$\beta$-Turn

A tight four-amino-acid motif that reverses the direction of a polypeptide chain by $180^\circ$ to connect antiparallel $\beta$-strands, commonly containing proline at position 2 and glycine at position 3.

Isoelectric focusing

An analytical electrophoresis technique that separates proteins across a stable $\text{pH}$ gradient in an electric field until each protein migrates to the specific $\text{pH}$ equal to its isoelectric point ($\text{pI}$).