Protein Structure and Amino Acids (Vocabulary Flashcards)

A set of vocabulary flashcards covering amino acids, protein structure levels, secondary/tertiary/quaternary structures, domains/motifs, conformational changes, allostery, ligands, covalent modifications, and denaturation.

Amino acids

20 different building blocks used in proteins; all are alpha amino acids; glycine is not chiral; proline is an imino acid; side chains determine each amino acid’s properties.

Alpha amino acid

Standard form of amino acids in proteins with the amino group on the alpha carbon.

Proline (imino acid)

Unique amino acid whose amino group forms a ring with its side chain, classed as an imino acid.

Glycine

The simplest amino acid with no chiral center; achiral.

L- isomers

Natural amino acids in proteins are the left-handed (L) enantiomers.

Side chain

The variable R group that defines amino acid identity and chemical properties.

Hydrophobic (nonpolar) side chains

Nonpolar R groups, usually hydrocarbon-rich, lacking charge or dipole.

Hydrophilic (polar) side chains

Polar or charged R groups that interact with water or have dipoles.

Charged amino acids

Amino acids with side chains carrying a net negative or positive charge (acidic or basic).

Dipole

Separation of charge within a molecule; important in polar side chains and certain residues.

Histidine, Tyrosine, Tryptophan

Amino acids with large hydrocarbon portions that also contain dipoles, making classification tricky.

Three-letter code

Abbreviation for amino acids using the first three letters of the name.

One-letter code

Single-letter abbreviations for amino acids (often the first letter; adjustments made to avoid duplicates).

Polar (neutral) R groups

Hydrophilic, polar side chains such as Asn, Gln, Ser, Thr, Tyr.

Asparagine (Asn)

Polar, uncharged amide-containing side chain.

Glutamine (Gln)

Polar, uncharged amide-containing side chain.

Serine (Ser)

Polar, uncharged with a hydroxyl group.

Threonine (Thr)

Polar, uncharged with a hydroxyl group.

Tyrosine (Tyr)

Aromatic, polar residue with a phenolic –OH group.

Lysine (Lys)

Basic amino acid with a positively charged side chain.

Arginine (Arg)

Basic amino acid with a positively charged guanidinium group.

Histidine (His)

Basic amino acid with an imidazole side chain; can be positively charged depending on pH.

Aspartate (Asp)

Acidic amino acid with a negatively charged carboxylate side chain.

Glutamate (Glu)

Acidic amino acid with a negatively charged carboxylate side chain.

Hydrophobic amino acids (general)

A group of nonpolar amino acids including alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, methionine, cysteine, glycine.

Alanine (Ala)

Hydrophobic amino acid with a simple methyl side chain.

Valine (Val)

Hydrophobic amino acid with an isopropyl side chain.

Leucine (Leu)

Hydrophobic amino acid with an isobutyl side chain.

Isoleucine (Ile)

Hydrophobic amino acid with a sec-butyl side chain.

Proline (Pro)

Hydrophobic amino acid with a cyclic side chain; contributes to structure due to rigidity.

Phenylalanine (Phe)

Hydrophobic amino acid with a benzyl phenyl group.

Tryptophan (Trp)

Hydrophobic amino acid with a large indole ring.

Methionine (Met)

Hydrophobic amino acid with a thioether side chain.

Cysteine (Cys)

Hydrophobic-ish amino acid with a thiol group; can form disulfide bonds.

Glycine (Gly)

Smallest amino acid; nonpolar, highly flexible; not chiral.

Primary structure

Linear sequence of amino acids in a protein; defined by the DNA-encoded order; connected by peptide bonds.

Peptide bond

Covalent bond between the carbonyl carbon of one amino acid and the amino nitrogen of the next; formed by dehydration (loss of water).

N-terminus

Free amino end of a polypeptide; numbered as residue 1.

C-terminus

Free carboxyl end of a polypeptide.

Protein

A biologically active molecule that may consist of one or more peptide chains; can have attached carbohydrates, lipids, cofactors or metal ions; primary structure is genetically coded.

Secondary structure

Local folding patterns stabilized by hydrogen bonds between C=O and N–H dipoles; includes alpha-helix and beta-sheet.

a-Helix

Right-handed coiled structure with 3.6 residues per turn; hydrogen bonds between every fourth residue; side chains project outward.

Beta-sheet

Secondary structure formed by hydrogen bonds between adjacent strands; can be parallel or antiparallel; antiparallel is stronger.

Collagen triple helix

Three strands form a left-handed triple helix; glycine repeats and hydroxyproline stabilize the structure.

Tertiary structure

Overall 3D folding of a polypeptide driven by side-chain interactions; hydrophobic core; can be stabilized by multiple bond types.

Hydrophobic interactions

Driving force for folding; nonpolar residues cluster away from water, forming a hydrophobic core.

Disulfide bonds

Covalent bonds between cysteine residues (cystine) that can be intra- or inter-chain.

Electrovalent bonds (Salt bridges)

Ionic interactions between oppositely charged side chains (acidic with basic residues).

Hydrogen bonds (tertiary)

Hydrogen bonds between polar, hydrogen-bond-capable side chains and groups.

Van der Waals forces

Weak, non-covalent interactions that are numerous and contribute to packing in the folded protein.

Quaternary structure

Association of multiple peptide subunits into a functional protein; interchain interactions and sometimes interchain disulfide bonds.

Subunit

A single polypeptide chain that can assemble with others to form a protein complex.

Monomer

A single protein subunit; can exist alone or as part of a larger oligomer.

Dimer

A protein formed by two subunits bound together.

Domain

A discrete globular region within a protein with its own binding properties and function.

Motif

A recurring, recognizable structural element within proteins (e.g., b-barrel, helix-turn-helix, zinc finger) that confers specific properties.

Immunoglobulin G (IgG)

An antibody example that contains domain structures recurring in proteins.

b-barrel

Beta-barrel motif formed by beta-strands creating a sheet that twists into a barrel-like shape.

Helix-turn-helix

DNA-binding motif with an alpha-helix connected to another by a short turn; common in DNA-binding proteins.

Zinc finger

DNA-binding motif stabilized by a zinc ion coordinating with cysteine/histidine residues.

Conformational change

Rearrangement of a protein’s structure in response to changes in environment or ligand binding.

pH

Measure of acidity/alkalinity that influences charge states and protein structure.

Allostery

Regulation of protein activity via binding of a ligand at a site other than the active site, causing conformational change.

Ligand

Any non-protein molecule that binds to a protein’s binding site and can regulate activity.

Covalent modification

Post-translational alteration of a protein, often reversible, such as phosphorylation.

Phosphorylation

Attachment of a phosphate group to Ser/Thr/Tyr residues to regulate activity; reversible by enzymes.

Denaturation

Disruption of a protein’s 3D structure due to heat or extreme conditions, often leading to aggregation.

Coagulation

Irreversible aggregation of proteins following denaturation.

Temperature effects on denaturation

Different proteins denature at different temperatures (e.g., some near 50°C, others near 100°C).

pH extremes and denaturation

Most proteins denature at very low pH (around 2–3) or very high pH (around 12).