BIO1010 Module 6: Macromolecules - Proteins and Enzymes

Definitions

• Denaturation:

  • The process in which a protein loses its native structure and function due to the disruption of bonds and interactions that stabilize its structure. Common causes include changes in temperature, pH, and chemical exposure.

• Specificity:

  • A characteristic of enzymes that allows them to catalyze a specific reaction or set of reactions based on the specific substrate they bind to. This specificity arises from the unique shape of the enzyme's active site, which matches the substrate's shape.

• Peptide bond:

  • A covalent bond formed between two amino acids during a dehydration synthesis reaction, linking the amino group of one amino acid to the carboxyl group of another. This bond is fundamental in forming the primary structure of proteins.

Basic Structure of an Amino Acid

• An amino acid consists of three principal components:
  • A central carbon atom (C)
  • An amino group (-NH2)
  • A carboxyl group (-COOH)
  • A hydrogen atom (-H)
  • A variable R group (side chain) that determines the identity and properties of the amino acid.

Levels of Protein Structure

1. Primary Structure:

   • Sequence of amino acids in a polypeptide chain. This sequence is determined by the genetic code and dictates the higher levels of protein structure.

2. Secondary Structure:

   • Local folding of the polypeptide chain into structures such as alpha helices and beta pleated sheets, stabilized by hydrogen bonds between the backbone atoms.

3. Tertiary Structure:

   • The overall three-dimensional structure of a polypeptide, resulting from interactions between the R groups of the amino acids. Includes various types of bonds (disulfide bridges, ionic bonds, hydrogen bonds, van der Waals interactions).

4. Quaternary Structure:

   • The assembly of multiple polypeptide chains (subunits) into a single functional protein. Not all proteins have quaternary structures.

Types of Bonds in Protein Structure

• Hydrogen Bonds:
  • Important for maintaining secondary structure and tertiary structure.
• Ionic Bonds:
  • Formed between positively and negatively charged R groups.
• Disulfide Bridges:
  • Covalent bonds that form between cysteine residues, providing stability to the protein structure.
• Hydrophobic Interactions:
  • Nonpolar amino acids tend to cluster away from water, stabilizing the overall shape.
• Van der Waals Forces:
  • Weak attractions between all atoms that help stabilize the structure when in close proximity.

Enzyme Functionality

• Optimal Temperature and pH:

  • Enzymes have optimal conditions under which they function most efficiently.

  • Temperature:

  • At low temperatures, molecular movement slows, reducing enzyme activity. High temperatures can lead to denaturation, disrupting the active site.

  • pH:

  • Each enzyme has an optimal pH range; deviations can affect ionization of side chains, altering the enzyme’s shape and function.

Enzyme-Catalyzed Reaction Diagram

• The diagram should include the following labels:
  • Enzyme: The protein that catalyzes the reaction.
  • Active Site: The specific region where substrate molecules bind to the enzyme.
  • Substrate(s): The reactant molecules that the enzyme acts upon.
  • Product(s): The molecules resulting from the enzymatic reaction after the substrate has been converted.