Proteins

Lecture Overview

  • Instructor: Prof. Richard Waites

Learning Outcomes

  • Understanding Biochemists' Goals: Reflect on what biochemists can achieve and the significance of their work.

  • Amino Acids and Proteins: Recognize key aspects of amino acid and protein structure and function.

  • Chemistry's Role: Note the importance of chemistry teaching in developing as a biochemist.

  • Enzymes and Reactions: Understand the relevance of amino acids and proteins in enzymes and biochemical reactions.

  • Metabolism: Acknowledge how learning about amino acids and proteins is crucial for metabolic processes.

Protein Structure Levels

  • Four Levels of Structure:

    • Primary Structure: Sequence of amino acids in the protein.

    • Secondary Structure: Localized folding patterns, includes alpha helices and beta sheets.

    • Tertiary Structure: The overall 3D arrangement of the polypeptide.

    • Quaternary Structure: Association of multiple polypeptides into a multi-subunit protein.

Peptide Bond Formation

  • Polypeptide: A series of amino acids linked by peptide bonds.

  • Amino Acid Definitions: In a polypeptide chain, amino acids are referred to as residues.

  • Polarity: N-terminus (start) and C-terminus (end).

  • Bond Processes:

    • Peptide Bond Hydrolysis: Breaking of peptide bonds.

    • Condensation Reaction: Formation of peptide bonds.

Peptide Bond Characteristics

  • Double Bond Character: Peptide bond exhibits partial double bond character that restricts rotation.

  • Bond Lengths:

    • Typical C-N distance in peptide bonds = 1.32Å

    • Expected single bond = 1.49Å

    • Expected double bond = 1.27Å

Backbone Conformations

  • Rotational Constraints:

    • The peptide bond cannot rotate, but adjacent bonds can.

    • Angle Definitions:

      • Psi (Ψ): angle of Cα-C bond.

      • Phi (Φ): angle of N-Cα bond.

    • Steric Limitations: 77% of potential psi and phi combinations do not occur due to steric hindrance.

Ramachandran Plot

  • Utility: Tool for assessing protein structure quality and aiding structural modeling.

Insulin History

  • Medical Milestones:

    • 1922: First medical use by Banting, Best, and Macleod (Nobel Prize in 1923).

    • 1940: Sequenced by Sanger (Nobel Prize in 1958).

    • 1969: 3D structure determined by X-ray crystallography by Dorothy Hodgkin.

    • 1977: Rosalyn Yarrow's radioimmunoassay method proved the cause of type 2 diabetes.

    • 1982-2005: Development of recombinant and modified insulins for treatment.

Nobel Prize Highlights

  • Sanger's Work:

    • Awarded in 1958 for studies on protein structure, particularly insulin.

    • Developed methods for sequencing and identifying polypeptide chains.

  • Hodgkin's Contributions:

    • Awarded in 1964 for X-ray crystallography determining structures of complex molecules.

Insulin and Structural Biology

  • Insulin Dimer Structure: Insights into fast-acting and slow-acting insulin mechanisms.

  • Structural Modifications: Techniques used to design insulin with altered absorption rates.

Protein Secondary Structure

  • Hydrogen Bonding: Stabilization through N-H and C=O interaction in peptide bonds.

  • Helices:

    • α-Helices

      • Formed by specific hydrogen bonding patterns.

      • Consists of 3.6 amino acids per turn.

    • β-Sheets:

      • Formed by parallel or anti-parallel strands held together by hydrogen bonds.

Gene Duplication and Evolution

  • Types of Homologous Genes:

    • Orthologous: Different species with shared ancestry.

    • Paralogous: Genes within the same organism that arose from duplication.

    • Pseudogenes: Non-functional copies of genes.

    • Mechanisms of Gene Duplication: Subfunctionalization and neofunctionalization.

Cofactors and Modifications

  • Types of Cofactors:

    • Prosthetic Groups: Permanently attached, e.g., NAD+.

    • Coenzymes: Temporary associations.

    • Metal Ions.

  • Post-Translational Modifications: Includes glycosylation, phosphorylation, acetylation, and more.

Glossary of Key Terms

  • Key terms include: acetylation, cofactor, covalent bond, dipole, glycosylation, hydrogen bond, post-translational modification, secondary structure, tertiary structure, quaternary structure.

Bioinformatics & Sequence Conservation

  • Importance of analyzing conserved sequences across different species to understand protein function and evolution.