Amino Acids, Peptides, and Protein Structure

Flashcards covering the vocabulary of amino acids, peptide bonds, levels of protein structure, and the thermodynamics of protein folding based on the lecture notes.

Isoelectric Point (pI)

The pH at which a molecule has a net charge of zero; for small peptides, it is calculated based on the pKa values of ionizable groups.

Salt bridges

Ionic interactions between charged groups (such as "+" Argentinine/Lysine and "-" Aspartate/Glutamate) that are essential for biomolecular interactions.

Hydroxylysine and hydroxyproline

Modified amino acids found in collagen that have been modified by the addition of hydroxyl groups.

Carboxyglutamate

A modified amino acid found in blood-clotting proteins characterized by an extra carboxylate addition.

Phosphorylated amino acids

Modified amino acids found in signaling proteins that have undergone the addition of phosphate groups.

Epinephrine

An important amino acid derivative originating from tyrosine.

Histamine

An amino acid derivative originating from histidine.

Serotonin

An amino acid derivative originating from tryptophan.

Peptide (Amide) Bond

A linkage between amino acids catalyzed by ribosomes; it has partial double bond character, making it rigid and planar.

Resonance of the peptide bond

The sharing or delocalization of electrons over the C, N, and O atoms, resulting in a shorter C-N bond and planar geometry.

Trans isoform

The favored configuration of the peptide bond because the alternate cis isoform leads to steric clashes.

$\Phi$ (phi) bond

The rotatable bond in the polypeptide backbone between the nitrogen and the $\alpha$-carbon ($N-C_{\alpha}$).

$\Psi$ (psi) bond

The rotatable bond in the polypeptide backbone between the $\alpha$-carbon and the carbonyl carbon ($C_{\alpha}-C$).

$\omega$ (omega) bond

The rigid, non-rotatable peptide bond between the carbonyl carbon and the nitrogen ($C-N$).

Residue

An individual amino acid within a peptide or protein chain.

Oligopeptide

A molecule containing fewer than 10 amino acids linked together.

Polypeptide

A molecule containing more than 10 amino acids linked together.

Protein

A functional molecule consisting of one or more polypeptides.

Primary Structure

The unique sequence of amino acids in a peptide or polypeptide, showing all covalent bonds.

Secondary Structure

Sub-structures formed by hydrogen bonds between atoms in the protein backbone, such as $\alpha$-helices and $\beta$-strands.

Tertiary Structure

The three-dimensional arrangement of all residues in a single polypeptide, stabilized by the hydrophobic effect, salt bridges, and disulfide bonds.

Quaternary Structure

The vertical arrangement and interaction of two or more polypeptide subunits in a complex.

$\alpha$-helix

A right-handed helical secondary structure stabilized by hydrogen bonds parallel to the helical axis with R-groups pointing outwards.

Pitch

The distance between two identical points on adjacent turns of an $\alpha$-helix, which is $5.4\,\text{\AA}$.

Rise

The distance per residue in an $\alpha$-helix, calculated as pitch divided by residues per turn ($1.5\,\text{\AA}$).

Helical Wheel

A representation looking down the helical axis of an $\alpha$-helix used to identify hydrophilic and non-polar faces.

$\beta$-strands

Extended polypeptide structures that form $\beta$-pleated sheets, stabilized by perpendicular hydrogen bonds between backbone atoms.

$\beta$-turn

A 4-amino acid motif commonly containing proline and glycine that allows the polypeptide chain to reverse direction.

Ramachandran Plot

A plot showing the allowed, borderline, and unallowed torsion angles ($\Phi$ and $\Psi$) for secondary structures.

Random Coil

Flexible regions of an amino acid sequence that do not adopt a uniform secondary structure.

Anfinsen's Hypothesis

The theory that the primary structure of a protein contains all the information necessary to drive its folding into the native state.

Hydrophobic Effect

The primary driving force of protein folding where non-polar side chains are forced into the interior core to avoid water.

Homo-oligomer

A multi-subunit protein complex in which all polypeptide subunits are identical.

Hetero-oligomer

A multi-subunit protein complex composed of two or more different types of subunits, such as hemoglobin.

Protomer

The repeating structural unit in a quaternary protein complex, which may consist of one or more subunits.

Globular Proteins

Spherical or elliptical proteins that are generally soluble in water and play enzymatic or regulatory roles.

Fibrous Proteins

Rod-shaped proteins that are insoluble in water and play structural and protective roles, such as collagen and keratin.

Simple Proteins

Proteins composed only of amino acids.

Conjugated Proteins

Proteins containing a non-peptide prosthetic group required for their function.

Apo-protein

A conjugated protein that is currently missing its required prosthetic group.

Holo-protein

A conjugated protein with its prosthetic group present.

Metamorphic Protein

A protein that can exist in two or more distinct low-energy folded states, such as the prion protein.

Intrinsically Unstructured Proteins (IUPs)

Proteins that lack a stable structure, often containing few hydrophobic amino acids and high percentages of hydrophilic residues like glycine and proline.

Chaperones

Protein complexes that assist in the proper folding of new proteins or the refolding of denatured proteins.