Protein Structure Overview

Flashcards covering key terms and concepts from protein structure and folding.

Primary Structure

The linear sequence of amino acids in a polypeptide chain, from the N-terminal to the C-terminal.

Secondary Structure

Regular, repeated conformation along short sections of a polypeptide, including α-helices and β-sheets.

Tertiary Structure

The overall three-dimensional shape of a polypeptide, determined by interactions among side chains.

Quaternary Structure

The arrangement of multiple polypeptide subunits in a protein, stabilized by non-covalent interactions.

α-helix

A helical structure in proteins stabilized by hydrogen bonds, typically consisting of 3.6 amino acids per turn. Side chains point outward from the helix

β-sheet

A sheet-like structure formed by hydrogen bonding between amide and carbonyl groups of peptide bonds from opposite strands of a polypeptide. They can be antiparallel (H-bonds run opposite) or parallel (H-bonds run in the same direction).

Ramachandran Plot

A graphical representation of the φ (phi) and ψ (psi) dihedral angles of amino acids in protein structures.

Protein Folding

The process by which a protein assumes its functional shape or three-dimensional conformation.

Hydrophobic Core

A region in proteins where hydrophobic amino acid side chains are buried to avoid contact with water.

C-terminal

The end of a polypeptide chain that has a free carboxyl group (-COOH).

N-terminal

The end of a polypeptide chain that has a free amino group (-NH2).

Peptide Bond

The covalent bond that links two amino acids together in a protein.

Disulfide Bridges

Covalent bonds formed between the sulfur atoms of cysteine residues in proteins, contributing to tertiary structure.

Protein Misfolding

The incorrect folding of proteins that can lead to various diseases, such as Alzheimer's and Parkinson's.

Circular Dichroism (CD) Spectroscopy

A technique used to measure the chiral properties of proteins, especially to determine secondary structure content. Measures the difference in absorption between left and right-handed polarized light

Hydrogen Bonding

A weak bond between a hydrogen atom and an electronegative atom, significant in stabilizing protein structures.

Fibrous Proteins

Proteins characterized by elongated structures, often providing strength and support, such as collagen and keratin. Mechanically strong, water-insoluble.

Globular Proteins

Proteins that are spherical and soluble in water, having diverse functions within biological systems.

Domain

A combination of different motifs. A distinct functional and structural unit within a protein that can evolve, function, and exist independently.

Chaperones

Proteins that assist the folding of other proteins to achieve their functional three-dimensional shapes.

β-turns

Connecting elements allowing the polypeptide chain to reverse direction, stabilized by a H-bond from a carbonyl oxygen to amide 3 residues down the sequence

Random coil

Irregular arrangement of the polypeptide chain

psi angle

Angle around the alpha carbon - carbonyl carbon bond

phi angle

angle around the alpha carbon - amide nitrogen bond

Structural motifs (folds)

Specific arrangement of 2 or more secondary structure elements + connections, recurring structures in numerous proteins, indicative of a particular 3D architecture and associated with specific function.

β-α-β loop

2 parallel beta strands joined by an alpha helix through connect hoops

Beta harpin

2 beta strands that look like a hairpin

Greek key

4 adjacent antiparallel strands and their linking loops

Helix-turn-helix

2 alpha helices connect by a short beta turn

Beta barrel

A beta sheet that coils and loops forming a closed structure in a barrel shape

Collagen

Found in connective tissue. Secondary structure is a left-handed, repeating tripeptide unit. tertiary and quaternary structures are right handed twisting of 3 separate polypeptides

Alpha-keratin

Key structural material of hair. Rich in hydrophobic residues It forms coiled-coil structures and has a high tensile strength.

X-ray crystallography

Process used to determine the atomic structure of proteins by diffracting X-rays through a crystal.

Nuclear Magnetic Resonance (NMR)

Carried out on protein in solution analyzed with NMR. This technique provides information about the protein's structure, dynamics, and interactions in a native-like environment.

Cryo-electron microscopy (cryo-EM)

Protein is frozen and observed in 2 dimensions with the electron microscope