chapter 2 Protein Structure and Properties

Flashcards covering protein structure definitions, torsion angles, levels of protein structure, secondary structure motifs, Ramachandran plot parameters, and specific protein examples from Chapter 2.

Polypeptide

A linear chain of amino acid residues linked by peptide bonds, extending from the amino-terminal (N-terminal) residue to the carboxyl-terminal (C-terminal) residue.

Peptide-Bond Resonance Structures

Resonance representations of the peptide group demonstrating partial double-bond character between the carbonyl carbon ($\text{C}$) and amide nitrogen ($\text{N}$), which restricts rotation around the bond.

Torsion Angle Phi ($\phi$)

The angle of backbone rotation around the bond between the amide nitrogen and the alpha carbon (\text{N-C}_\n\alpha).

Torsion Angle Psi ($\psi$)

The angle of backbone rotation around the bond between the alpha carbon and the carbonyl carbon ($\text{C}_\alpha\text{-C}$).

Ramachandran Plot

A two-dimensional plot displaying the torsion angles $\phi$ versus $\psi$ that indicates sterically allowed and disfavored backbone conformations for amino acid residues.

Primary Structure ($1^\circ$)

The linear sequence of amino acid residues in a polypeptide chain.

Secondary Structure ($2^\circ$)

The local spatial arrangement of the main chain backbone atoms, forming regular repeating structures such as $\alpha$-helices and $\beta$-strands.

Tertiary Structure ($3^\circ$)

The overall three-dimensional folding pattern and spatial arrangement of all atoms in a single polypeptide chain.

Quaternary Structure ($4^\circ$)

The three-dimensional arrangement and interaction of multiple polypeptide chains (subunits) forming a multi-subunit protein complex.

$\alpha$-Helix

A coiled secondary structure motif stabilized by hydrogen bonds between the carbonyl oxygen ($\text{C=O}$) of residue $i$ and the amide hydrogen ($\text{N-H}$) of residue $i+4$ along the backbone from N-terminus to C-terminus.

Right-Handed $\alpha$-Helix Torsion Angles

The favored backbone torsion angle values for a right-handed $\alpha$-helix, centered at $\phi = -57^\circ$ and $\psi = -47^\circ$.

$3_{10}$-Helix

A helical secondary structure type stabilized by hydrogen bonds between the carbonyl oxygen of residue $i$ and the amide hydrogen of residue $i+3$.

$\beta$-Strand

An extended polypeptide chain conformation with torsion angles centered around $\phi = -119^\circ / -139^\circ$ and $\psi = +113^\circ / +135^\circ$.

$\beta$-Sheet

A secondary structure formed by interchain hydrogen bonds between $\text{N-H}$ and $\text{C=O}$ groups of adjacent parallel or antiparallel $\beta$-strands.

Reverse Turn (or $\beta$-turn)

A tight structural feature involving four residues, where a hydrogen bond forms between the carbonyl oxygen of residue $i$ and the amide nitrogen of residue $i+3$, directing the chain back toward the protein interior.

Lactoferrin

An iron-binding protein composed of distinct domains that demonstrates structural flexibility by changing from an open conformation to a closed conformation upon binding iron.

Collagen

A fibrous structural protein characterized by repeating amino acid triplets (such as $\text{-Gly-Pro-Hyp-}$) that fold into a triple-helical structure.