W17 L2 - Protein Structure and Folding

Flashcards reviewing protein structure, folding, and related concepts.

Primary Structure of a Protein

The order of the amino acid sequence, with condensation reactions forming peptide bonds. Rotation around the peptide bond is restricted due to its partial double bond character.

Backbone of a Peptide

A typical sequence of N-C alpha-carboxy-N-C alpha-carboxy.

Writing Proteins

Amino terminus (amino group) to the left, carboxy terminus (carboxylic group) to the right.

Primary Structure Determination

Governed by peptide bonds as interactions.

Secondary Structure

Alpha helix and beta sheets (beta pleated sheets).

Stabilization of Secondary Structures

Hydrogen bonds in the backbone stabilize the structures.

Alpha Helix Side Chains

Side chains stick out to the sides.

Beta Sheet Orientations

Parallel or antiparallel; amino acid side chains stick out at opposite sides.

Tertiary Structure

Interactions between the side chains of the amino acids.

Interactions in Tertiary Structure

Electrostatic interactions, hydrogen bonds, covalent bonds (disulfide bonds between cysteine residues).

Disulfide Bonds

They can only form under oxidizing conditions, not usually found in cytoplasmic proteins.

Hydrophobic Effect

Not a true interaction, but an effect where hydrophobic amino acids aggregate inside a protein to avoid water.

Quaternary Structure

Two or more proteins interacting to form a complex and a functional molecule. Interactions are the same as in tertiary structure.

Homodimer

Two protein chains that are exactly the same that form an interaction with each other.

Heterodimer

Two chains that are not the same protein that form an interaction with each other.

Hemoglobin

Four identical subunits (homotetramer).

Incorrect Protein Structure

The protein will not be functional.

Anfinsen's Folding Dogma

All the information about the right structure of the protein is given in the primary sequence (order of amino acids).

Leventhal's Paradox Resolution

The protein does not check every single interaction; folding starts immediately after the protein emerges from the ribosome (cotranslational folding).

Folding Process

Starts immediately after protein emerges from ribosome.

Molecular Chaperones (Folding Helpers)

Other proteins that help a protein to fold correctly or protect it from making wrong interactions.