Protein Structure & Function - Quick Notes

What Proteins Do

  • Crucial to most cellular functions: \text{catalysis},\ \text{defense (antibodies)},\ \text{movement},\ \text{signaling},\ \text{structure},\ \text{transport}.
  • Diversity in function arises from varying size, shape, and chemical properties of amino acids.

Structure of Amino Acids

  • Subunits of proteins: 20 types.
  • Common structure: \mathrm{H_2N-CH(R)-COOH}
  • At physiological pH 7.4, amino & carboxyl groups ionize to \mathrm{NH_3^+} and \mathrm{COO^-}, aiding solubility and reactivity.

Side Chains (R-groups) and Water Interaction

  • 20 different side chains (R-groups) differ in size, shape, reactivity, and water interaction.
  • Nonpolar R-groups: hydrophobic; coalesce in water.
  • Polar R-groups: hydrophilic; form H-bonds; dissolve in water.

Interactions with Water (Hydrophilicity/Hydrophobicity)

  • Hydrophobic: highly/very nonpolar
  • Hydrophilic: polar or charged; interact with water
  • Ranking of water interaction influences protein folding and solubility.

Monomers and Polymers

  • Amino acids are monomer subunits; proteins are polymers (macromolecules).
  • Polymerization requires energy (nonspontaneous).

Polymerization and Dehydration Synthesis

  • Monomers polymerize by dehydration (condensation) reactions — release a water molecule.-
  • Result: peptide bonds link amino acids.

Hydrolysis

  • Reverse reaction: water is added; polymers are broken into monomers.

The Peptide Bond

  • Condensation reaction bonds the carboxyl group of one amino acid to the amino group of another: a peptide bond.

Polypeptide Backbone Characteristics

  • 3 characteristics of peptide bonds:
    • R-group orientation: side chains interact with each other or with water.
    • Directionality: left end is the N-terminus; right end is the C-terminus.
    • Flexibility: bonds around the peptide bond can rotate; the chain is flexible.

Proteins Are the Most Diverse Class of Molecules

  • Examples of protein types: Collagen (fibrous; structural support), TATA box–binding protein, Porin, Trypsin.
  • Proteins show remarkable diversity in shape and function.

Levels of Protein Structure

  • Four levels: Primary, Secondary, Tertiary, Quaternary.
  • Primary: unique amino acid sequence.
  • Secondary: regular folding patterns stabilized by hydrogen bonds along the backbone.
  • Tertiary: overall 3D shape from interactions among R-groups and backbone.
  • Quaternary: assembly of two or more polypeptide subunits.

Primary Structure

  • Primary structure dictates folding into higher-order structures.
  • Normal sequence example: Pro — Glu — Glu — … (sequence determines function).

Secondary Structure

  • Hydrogen bonds between C=O and N–H along the backbone.
  • Forms: \alpha-helices and \beta-pleated sheets; contribute to protein stability.

Tertiary Structure

  • Interactions among R-groups bend the backbone into the 3D shape.
  • Includes weak electrical interactions among hydrophobic side chains.

Quaternary Structure

  • Bonding/interactions between multiple polypeptide subunits.
  • Examples: Cro protein dimer; Hemoglobin tetramer.

Folding and Function

  • Protein folding is spontaneous and yields a more stable structure.
  • Denatured proteins are typically nonfunctional.
  • Molecular chaperones assist proper folding.

Prions

  • Prions are amino acid sequences that misfold and induce misfolding of normal proteins, causing diseases (e.g., mad cow disease).

Why Are Enzymes Good Catalysts?

  • Enzymes are proteins that function as catalysts.
  • Substrates are the reactants in enzyme-catalyzed reactions.
  • The active site is the location on the enzyme where substrates bind and react.

Enzyme Specificity and Action

  • Enzymes bring substrates into precise orientation to increase reaction likelihood.
  • Each enzyme is specific for one type of reaction; active sites are complementary to substrates.

Quick Concept Recap

  • Peptide bonds link amino acids; primary structure determines higher-order structure.
  • Hydrogen bonding stabilizes secondary structure; hydrophobic effects drive tertiary structure.
  • Quaternary structure arises from assembling multiple subunits.
  • Mutations in primary structure can alter function (e.g., sickle cell mutation in β-globin).
  • Enzymes accelerate reactions via the active site and substrate orientation.

Note

  • For hydrolysis and dehydration reactions, remember:
    • Dehydration: \text{monomer} + \text{monomer} \rightarrow \text{dimer} + H_2O
    • Hydrolysis: \text{dimer} + H_2O \rightarrow \text{monomer} + \text{monomer}