Macromolecules: Polypeptides and Proteins part 3

Polymers and Monomers

  • Polymers: Large molecules consisting of many repeating units.
    • The prefix "poly" means many, and "mers" refers to units.
    • Examples include polysaccharides, nucleic acids, and proteins.
  • Monomers: Single units or building blocks that make up polymers.
    • The identity of the monomer varies depending on the polymer being built.
      • Sugars for polysaccharides (carbohydrates).
      • Nucleotides for nucleic acids.
      • Amino acids for proteins.

Polypeptides and Proteins

  • Polypeptides are long chains of amino acids linked together covalently.
  • Proteins are formed when these polypeptide chains take on a specific structure.
  • A protein may consist of one or more polypeptide chains.
  • The terms "polypeptide" and "protein" are often used interchangeably, although there is a technical difference.

Variety of Macromolecules

  • Cells contain thousands of different macromolecules.
  • A vast variety of polymers can be created from a limited set of monomers.

Dehydration Reaction (Condensation Reaction)

  • This reaction involves the attachment of monomers to a growing chain with the removal of a water molecule.
  • It is also known as a condensation reaction.
  • The general equation is monomer + growing\ chain \rightarrow growing \ chain \ with \ one \ more \ monomer + H_2O.
  • An enzyme facilitates this process.

Enzymes

  • Enzymes are specialized macromolecules that act as catalysts.
  • They speed up specific reactions without being altered or used up in the process.
  • Enzymes can catalyze the same reaction sequentially.
  • Life as we know it would not be possible without enzymes.

Hydrolysis Reaction

  • This reaction involves the breakdown of polymers into monomers through the addition of water.
  • An enzyme is required for this process.
  • The general equation is polymer + H_2O \rightarrow monomer + shorter \ polymer.

Enzyme Nomenclature

  • Many enzymes have names ending in "-ase."
    • For example, polymerase and hydrolase.
  • Polymerases catalyze the formation of polymers.
  • Hydrolases use water to split polymers into monomers.

Protein Functions

  • Proteins perform a wide variety of functions within cells.
  • Examples of protein functions include:
    • Enzymes: Catalyzing biological reactions. Most enzymes are proteins, although some are made of RNA.
    • Defensive proteins: Protecting the body from pathogens (e.g., antibodies).
    • Storage proteins: Storing building blocks for other proteins (e.g., proteins in an egg).
    • Transport proteins: Facilitating the movement of molecules across cell membranes.
    • Signaling molecules: Acting as hormones to transmit signals between cells.
    • Receptor proteins:binding signaling molecules on the surface of cells.
    • Contractile proteins: Controlling movement (e.g., actin and myosin in muscles).
    • Structural proteins: Providing structure and support to cells (e.g., cytoskeleton).

Diversity of Proteins

  • Proteins are incredibly diverse in both structure and function.
  • The structure of a protein determines its function.

Amino Acids: Monomers of Proteins

  • All proteins are constructed from a set of 20 common amino acids.
  • Each amino acid has:
    • A carboxyl group (can act as an acid by donating a proton).
    • An amino group.
    • An alpha ($\alpha$) carbon.
    • A hydrogen atom.
    • A side chain (R group).
  • The alpha carbon is also known as an asymmetric carbon.
  • 19 out of 20 amino acids have the same general structure; one has a slightly different structure but behaves similarly.

Peptide Backbone

  • The shared components of amino acids (amino group, alpha carbon, and carboxyl group) form the backbone of the peptide.
  • The side chain (R group) is what varies between different amino acids.

Hydrophilic vs. Hydrophobic Amino Acids

  • Amino acids are classified as hydrophilic (water-loving) or hydrophobic (water-fearing) based on the properties of their side chains.
  • The side chains determine how amino acids will interact within a polypeptide chain and in the final folded protein.

Examples of Amino Acids

  • Hydrophobic Amino Acids:
    • Glycine (Gly, G): Simplest amino acid with a hydrogen atom as its side chain.
    • Alanine (Ala, A).
    • Valine (Val, V).
    • Leucine (Leu, L).
    • Isoleucine (Ile, I).
    • Tryptophan (Trp, W): Contains a double ring structure.
    • Phenylalanine (Phe, F).
    • Methionine (Met, M).
    • Proline (Pro, P): Has a slightly different structure because its amino group is attached to the side chain.
  • Hydrophilic Amino Acids:
    • Serine (Ser, S).
    • Threonine (Thr, T).
    • Tyrosine (Tyr, Y): Contains a hydroxyl group, making it polar.
    • Cysteine (Cys, C): Can be considered either hydrophilic or hydrophobic, depending on the context.
    • Glutamine (Gln, Q).
    • Asparagine (Asn, N).
  • Electrically Charged (Hydrophilic) Amino Acids:
    • Acidic (negatively charged):
      • Aspartic acid (Asp, D).
      • Glutamic acid (Glu, E).
    • Basic (positively charged):
      • Lysine (Lys, K).
      • Arginine (Arg, R).
      • Histidine (His, H).

Polarity of Amino Acids

  • Hydrophobic amino acids are least likely to interact with water.
  • Hydrophilic amino acids are most likely to interact with water.
  • Charged amino acids are highly hydrophilic.

Hydrocarbon Chains

  • Side chains that consist of only carbons and hydrogens are classified as Hydrophobic.
  • Valine, Isoleucine, and Leucine are examples of amino acids with Hydrocarbon Chains.