Recording-2025-03-14T13:43:42.605Z

Overview of Peptide Bonds and Protein Structure

• Basic Understanding of Peptides

  • Peptides are chains of amino acids linked by peptide bonds, which can rotate due to sigma bonds.

  • Orientation of Bonds:

    • Right hand represents bonds extending out of the page (commonly Hydrogen).

    • Left hand represents bonds going into the page (commonly R group).

  • Bond Rotation:

    • Peptide bonds can rotate but with certain restrictions due to steric hindrance, which affects the overall conformation of proteins.

    • Eclipsing and gouging interactions can be unfavorable for the peptide chain.

Primary and Secondary Structure

• Primary Structure:

  • Refers to the specific sequence of amino acids in the peptide chain.

  • Determines the overall folding and secondary structure based on favorable angles.

• Secondary Structures:

  • Include alpha helices and beta sheets formed through hydrogen bonding between carbonyl and amide groups of the backbone.

  • Ramachandran Plot:

    • Identifies allowable and forbidden angles (phi and psi) based on steric hindrance.

    • Green areas represent allowed configurations that lead to stable structures.

Alpha Helices

• Typically right-handed and very common in proteins.

• Characteristics:

  • Formed by hydrogen bonds between the backbone's carbonyl oxygen and the amide group of an amino acid four residues earlier.

  • Rise per turn: Approximately 1.5 Å per residue, with about 3.6 residues per turn, resulting in roughly 12 Å per turn.

  • Side chains protrude outward and can affect local stability and interactions.

  • Types:

    • Right-handed helices are predominant.

    • Left-handed helices are rare and found in specific proteins.

Beta Sheets

• Comprise of strands connected by hydrogen bonds.

• Types:

  • Antiparallel: Strands align N-C to C-N, with strong hydrogen bonding.

  • Parallel: Strands align N-C to N-C, with weaker hydrogen bonds due to angles.

• Average strand length is approx. 6-15 amino acids.

• Arrangement:

  • Generally twisted or folded, contributing to structural stability.

  • R groups alternate above and below the plane of the sheet, influencing overall structure.

Tertiary and Quaternary Structure

• Tertiary Structure:

  • Refers to the three-dimensional structure formed by folding of a single polypeptide chain.

  • Interactions include:

    • Hydrophobic interactions concentrating nonpolar residues in the protein core, promoting stability.

    • Electrostatic interactions and hydrogen bonding contribute to holding the folded structure stable.

• Quaternary Structure:

  • Involves multiple polypeptide chains coming together to form a functional protein.

  • Can enhance stability and functionality through cooperative interactions.

Protein Stability Factors

• Hydrophobic Effect:

  • Crucial for stability; burying nonpolar residues decreases exposure to water, increasing water entropy.

• Hydrogen Bonds:

  • Form between different regions of the same or different polypeptide chains, providing structural integrity.

• Disulfide Bonds:

  • Covalent bonds between cysteine residues help lock protein structures in place, facilitating correct folding.

  • They are more common in extracellular proteins due to oxidative environments.

Protein Modifications and Use in Research

• Green Fluorescent Protein (GFP):

  • Derived from jellyfish, used as a reporter gene to trace proteins within cells.

  • Can be attached to proteins of interest for visual tracking.

  • Is a 238 amino acid-long protein that emits fluorescence under UV light.

  • Requires proper folding in order to achieve fluorescence, typically housed in a barrel of beta sheets.

• Application:

  • Used extensively in molecular biology and cell biology to illuminate protein behavior and interactions in live cells.

Learning and Study Strategies

• Focus on understanding secondary structures and the overarching principles that govern protein folding.

• Utilize diagrams to visualize structures and key interactions.

• Review assignments and use them to guide your study topics.

• Engage with practice problems to reinforce concepts and relationships in protein structure.