Amino Acids & Protein Structure Essentials

Vocabulary flashcards covering amino acid identities, protein structure levels, bonding, and related biochemical concepts.

Alanine (Ala, A)

Non-polar, aliphatic amino acid.

Arginine (Arg, R)

Basic, positively charged amino acid.

Asparagine (Asn, N)

Polar amino acid with an amide-containing side chain whose hydrogens do not ionize with pH changes.

Aspartic Acid (Asp, D)

Hydrophilic, acidic, negatively charged amino acid; deprotonated form is aspartate.

Cysteine (Cys, C)

Polar amino acid containing a thiol (sulfhydryl) that can form disulfide bonds; only amino acid with R configuration.

Glutamic Acid (Glu, E)

Acidic, negatively charged amino acid; deprotonated form is glutamate.

Glutamine (Gln, Q)

Polar amino acid with an amide side chain.

Glycine (Gly, G)

Non-polar, aliphatic amino acid; the only achiral proteinogenic amino acid.

Histidine (His, H)

Basic, positively charged amino acid containing an aromatic imidazole ring often found in enzyme active sites.

Isoleucine (Ile, I)

Non-polar, aliphatic amino acid.

Leucine (Leu, L)

Non-polar, aliphatic amino acid.

Lysine (Lys, K)

Basic, positively charged amino acid.

Methionine (Met, M)

Relatively non-polar amino acid containing sulfur; one of two sulfur-bearing amino acids.

Phenylalanine (Phe, F)

Non-polar, aromatic amino acid.

Proline (Pro, P)

Non-polar, cyclic amino acid whose rigidity induces kinks; commonly found at helix starts and β-turns.

Serine (Ser, S)

Polar amino acid with a hydroxyl group.

Threonine (Thr, T)

Polar amino acid with a hydroxyl group.

Tryptophan (Trp, W)

Non-polar, aromatic amino acid.

Tyrosine (Tyr, Y)

Slightly polar, aromatic amino acid due to its phenolic –OH.

Valine (Val, V)

Non-polar, aliphatic amino acid.

Amphoteric

Able to act as both an acid and a base; property of amino acids.

Zwitterion

Molecule bearing both a positive and a negative charge simultaneously; typical form of amino acids at physiological pH.

Isoelectric Point (pI)

Average Pka1 and Pka2

The pH at which an amino acid carries no net charge.

Carboxylic acid 2.15

Amide 9.52

pI Calculation Rule

Average the two pKa values that correspond to the +1 and –1 charge states of the molecule.

Deprotonation Rule

When pH > pKa, the ionizable group is deprotonated; when pH < pKa, it is protonated.

Peptide Bond

Resonance-stabilized amide linkage joining amino acids; exhibits partial double-bond character.

Peptide Bond Formation

Condensation (dehydration) reaction that releases water.

Oligopeptide

Peptide consisting of ≤20 amino acid residues.

Polypeptide

Amino-acid chain longer than 20 residues.

Primary Structure

Linear sequence of amino acids held by peptide bonds.

Secondary Structure

Regular patterns (α-helices, β-sheets) stabilized by backbone hydrogen bonds.

Alpha Helix

Right-handed coil with 3.6 residues per turn and backbone H-bonds every fourth residue.

Beta Pleated Sheet

Sheetlike arrangement of peptide strands lying side by side, stabilized by H-bonds.

Proline’s Role in Secondary Structure

Its rigid ring introduces kinks, disrupting helices/sheets but stabilizing starts and turns.

Tertiary Structure

Three-dimensional folding driven by side-chain interactions: hydrophobic effect, H-bonds, salt bridges, disulfide bonds.

Quaternary Structure

Assembly of multiple tertiary subunits; enables stability, reduced genetic load, catalytic cooperation, and allostery.

Hydrophobic Effect

Non-polar residues bury inside proteins, increasing water entropy and driving spontaneous folding.

Solvation Layer

Ordered layer of solvent molecules surrounding a solute due to electrostatic interactions.

Fibrous Protein

Protein shaped as long strands or sheets.

Globular Protein

Protein with roughly spherical shape.

Conjugated Protein

Protein that contains a covalently bound prosthetic group essential for function.

Prosthetic Group

Covalently attached non-protein molecule (e.g., vitamin, metal ion) required for protein activity.

Glycoprotein

Protein with a carbohydrate prosthetic group.

Lipoprotein

Protein with a lipid prosthetic group.

Nucleoprotein

Protein with a nucleotide prosthetic group.

Subunit

Individual polypeptide chain within a quaternary protein complex.

Disulfide Bond

Covalent S–S linkage formed by oxidation of two cysteine residues.

Cystine

The disulfide-linked pair of cysteine residues.

Disulfide Bond Formation

Oxidation reaction joining two cysteines.

Peptide Drawing Direction

Written from N-terminus (left) to C-terminus (right).

N-Terminus

Free amino group at the beginning of a peptide chain.

C-Terminus

Free carboxyl group at the end of a peptide chain.

Sequencing

Laboratory determination of a protein’s primary structure, often via underlying DNA.

Amino Acid Titration Curve

Resembles two monoprotic curves (three if the side chain is ionizable).

High vs. Low pH Behavior

At high pH ionizable groups are deprotonated; at low pH they are protonated.

Disulfide Bond Disruption

β-Mercaptoethanol reduces S–S bonds, aiding protein denaturation.

Protein Structural Classes

Fibrous and globular proteins.

A amino acid structure

Ala

G amino acid structure

Gly

V amino acid structure

Val

L amino acid structure

Leu

M amino acid structure

Met

I amino acid structure

Iso

S amino acid structure

Ser

T amino acid structure

Thr

C amino acid structure

Cys

P amino acid structure

Pro

N amino acid structure

Asn

Q amino acid structure

Gln

K amino acid structure

Lys

R amino acid structure

Arg

H amino acid structure

His

D amino acid structure

Asp or Aspartic acid

E amino acid structure

Glu or Glutamic acid

F amino acid structure

Phe

Y amino acid structure

Tyr

W amino acid structure

Trp