lec-2-biological-polymers

Biological Polymers & Protein Structure

Overview of Proteins

  • Proteins are the most diverse biological molecules with numerous roles including:

    • Development

    • Protection

    • Structural function

    • Transport

    • Catalyzing reactions

    • Communication

Amino Acids

  • Polymers of proteins are composed of amino acids:

    • There are 20 different amino acids.

    • General structure of an amino acid includes:

      • Alpha carbon

      • Amino group (NH2)

      • Carboxyl group (COOH)

      • R group (side chain)

      • Hydrogen atom

Influence of pH on Protein Charge

  • As pH decreases, the concentration of protons increases, causing the protein's overall charge to become more positive.

  • The effects of pH are significant throughout the entire polypeptide chain, not just at the ends.

  • Basic amino acids:

    • Lysine (Lys)

    • Arginine (Arg)

    • Histidine (His)

  • Acidic amino acids (always referred to as acidic):

    • Aspartic acid (Asp)

    • Glutamic acid (Glu)

Hydrophobicity & Hydrophilicity

  • The side chains of amino acids significantly impact their interaction with water:

    • Hydrophobicity/Hydrophilicity is not binary but exists on a spectrum.

    • Polar covalent bonds promote hydrogen bonding (HYDROPHILIC).

    • Nonpolar covalent bonds involve equal electronegativity (HYDROPHOBIC).

  • Chemical groups important for amino acids:

    • Hydroxyl

    • Carbonyl

    • Carboxyl

    • Methyl

Peptides & Polymer Formation

  • A peptide is a short polymer of amino acids.

  • Dehydration Reaction: Synthesizing a polymer requires energy, involving:

    • Removing a hydrogen atom from Peptide #1

    • Removing a hydroxyl group from Peptide #2 to form a longer polymer.

  • Peptide Bond Formation: This results in new peptide bonds.

  • Hydrolysis: Breaking down a polymer involves:

    • Adding a water molecule to split the polymer.

Folding & Coiling of Polypeptides

  • Peptide bonds, due to electronegativity, have a partial double-bond character.

  • Bonds adjacent to the alpha carbon allow for rotation.

  • Polypeptides adopt a specific structure dictated by:

    • The need for the protein to function, which is inherently linked to its structure.

  • In an aqueous solution, the arrangement can be summarized as:

    • Polar side chains orient outward toward the aqueous environment.

    • Nonpolar side chains tuck inside away from water.

Information for Polypeptide Folding

  • The folding of polypeptides is driven by the intrinsic information embedded in the:

    • Amino acid sequence of the protein.

    • This sequence determines the final functional shape of the protein.