Proteins and Their Structure

Proteins

• Large molecules composed of amino acids
• Properties depend on the sequence of amino acids
• Fold into highly organized 3D structures
• The folding pattern is crucial to the function of the protein

4 Levels of Protein Structure

• Primary Structure: The unique and specific sequence of amino acids in a polypeptide chain

  • Joined by peptide bonds
  • Synthesized from mRNA using the genetic code
  • Begins at the amino end and terminates at the carboxyl end
  • Ultimately determines all properties of a protein

• Secondary Structure: Local structures, including folds, turns, α-helices, and β-sheets, held in place by hydrogen bonds

• Tertiary Structure:

  • Produces the 3D structure of the amino acid chain
  • The most stable structure in a given environment
  • Native structure is the biologically active form of a protein
  • Creates an active site for biological function
  • Ultimately dictated by the primary structure and how the amino acid chain folds

• Quaternary Structure:

  • Arrangement of polypeptide chains into a functional protein
  • Some proteins are assemblies of two or more chains
  • The way these chains are organized is called the quaternary structure
  • Hemoglobin, for example, consists of 4 subunits: 2 α chains (identical) and 2 β chains (also identical)

Amino Acids

• The building blocks of proteins
• 20 common amino acids
• Each amino acid consists of:
  • Central carbon atom
  • Amino group
  • Carboxyl group
  • Side [R] Chain
• Differences in side chains (R groups) distinguish the 20 different amino acids

Classification of Amino Acids

• Non-polar (hydrophobic) amino acids
• Polar (hydrophilic), uncharged amino acids
• Polar (hydrophilic), charged either positive or negative

Forces Stabilizing Tertiary Structure

• Hydrogen bonds - Very weak
• Salt bridges - Weak
• Hydrophobic interactions - Weak
• Disulfide bridges - Strong

Globular & Fibrous Proteins

• Globular Proteins:

  • 3D structure normally folds up in a ball
  • Hydrophilic R groups point outwards
  • Hydrophobic R groups point inwards
  • Soluble
  • Metabolic functions
  • Example: Hemoglobin, IgG

• Fibrous Proteins:

  • 2º structure does not fold up, they form fibers
  • Not surrounded by hydrophilic R groups
  • Insoluble
  • Structural functions
  • Example: Collagen, Keratin

Secondary Structures

• The two most important secondary structures are α-helices and β-sheets
• Both held together by hydrogen bonds between the N-H and C=O projecting from the main chain
• α-helix:
  • Rodlike structure
  • Stabilized by hydrogen bonds between NH and CO groups of the main chain
  • CO group of each amino acid is hydrogen bonded to the NH group of the amino acid
• β-sheets:
  • Stabilized by hydrogen bonds between NH and CO groups in different polypeptide strands
  • Hydrogen bonds most often form between the CO and NH groups of adjacent chains, either parallel or antiparallel, from different regions of the polypeptide

Hemoglobin

• Example of a protein with quaternary structure
• Consists of 4 subunits
• 2 α chains (identical) and 2 β chains (also identical)

Protein Structure Summary

• 1º: Linear sequence of amino acids and disulfide bonds
• 2º: Local structures: folds, turns, α-helices and β-sheets held in place by hydrogen bonds
• 3º: 3D arrangement of all atoms in a single polypeptide chain
• 4º: Arrangement of polypeptide chains into a functional protein