Proteins: Structure aand Function.

Reprise:

Principle of Macromolecular Organisation.
All macromolecules are constructed by polymerization of low molecular weight units.

• Concept 1: Biopolymers are formed from monomeric units.
• Concept 2: Macromolecules have different orders of structure.
• Concept 3: Macromolecules associate non-covalently to form supramolecular structures, organelles, cells.

• Primary structure is the linear sequence of amino acids
• Secondary structure is the local spacial arrangement the amino acid sequence
• Tertiary structure is the 3-dimensional folding of the secondary structure
• Quaternary structure is the supramolecular assembly of proteins.

Structure of protein determines its function.
What are the biological function of proteins?
from our previous discussions.......

• enzymes, biological catalysts
• transport myoglobin, hemoglobin
• storage proteins of seeds
• structural components, support and shape, extracellular matrix, tendons, cartilage, hair
• molecular motors, contraction, flagellae, muscle
• regulation,information transfer, signals, hormones
• protection, defense, immunoglobulins, blood clotting

Primary structure is the linear sequence of amino acids.

How are amino acids joined together?
What is the bond called?
What are the functional groups involved in its formation?
What are the chemical characteristics of the bond?

From our discussion of chemistry, covalently linked by an amide or peptide bond
joining the carboxyl group of one amino acid to the amine group of another
Chemical characteristics:

• double bond character
• planar
• restricted rotation
• trans

Secondary structure is the local spacial arrangement along the axis of the primary structure, along the axis of the amino acid sequence.

Which Nobel laureate in Chemistry proposed just two major types of secondary structure?
Linus Pauling, double Nobel laureate for *the nature of the chemical bond* and for peace, first described the secondary structure of proteins. This was a natural progression from his interests in the peptide bond in particular and chemical bonding in general.

Given the nature of the peptide bond, what assumptions must be made about secondary structure?
Assumptions Pauling made:

• do not violate the properties of the peptide bond
• maximize H-bonds within and between peptides.

• alpha helix
• beta sheet

Examples of alpha helix and beta sheet are found for two common proteins that form fibers:

• alpha helix: the protein keratin of hair: long lengths of alpha helix wound around each other in helical coiled coils: forms flexible and stretchy fiber.
• beta sheet: the protein fibroin of silk (and spider web silk): long stretches of beta sheet that form a strong, rigid, and inextensible fiber.

Tertiary structure is the 3-dimensional folding of the secondary structure

Keratin and silk are unusual because they are 100% a-helical or b-sheet
They have little 3-D structure because they form long fibers
Most proteins are globular and have complex 3-D conformations
Most proteins contain mixtures of a-helix and b-sheet
Two common globular proteins are Myoglobin (oxygen transport in muscle) and Hemoglobin (oxygen transport in blood). They are unusual globular proteins because they contain about 70% a-helix and no b-sheet (the other 30% forms turns and irregular structure that is ill-defined)

What forces stabilize the tertiary structure of globular proteins?

• Stabilized by very many weak non-covalent interactions.

• charge interactions
• H-bonds
• dipole interactions (weakest)

• The 3D structures are stable but flexible.
• The conformations of proteins can change, stabilized by many, energetically weak, non-covalent bonds.

Experiments of Anfinsen and coworkers.
Experimental design:

• unfold the 3-D structure of a protein then allow it to refold while measuring its function.
• use high concentrations of urea as the protein denaturant (a reagent that reversibly unfolds proteins)
• had to have measures of both protein structure and function
• for structure, used a physical measurement of light absorption
• for function, used an enzyme and measured its activity: the enzyme ribonuclease that hydrolyses RNA

• urea disrupts non-covalent bonds
• urea completely destroyed the tertiary and secondary structure with loss of enzyme activity
• but does not disrupt covalent bonds and the primary structure
• when they removed the urea the protein refolded
• and regained full biological function

Principle of Information Transfer
Central Dogma: the linear, sequential information of DNA is translated into the linear sequential information of proteins (primary structure) which specifies the 3-D spatial information of proteins (tertiary structure and function).

What drives the folding of proteins?

• self association and folding driven by laws of thermodynamics.
• hydrophobic amino acids on the inside, hidden from the solvent
• hydrophilic amino acids (uncharged but polar and charged groups) on the outside, interacting with solvent
• entropy very important

• a measure of the disorder in the system

• the hydrophobic effect
• protein folding hides the hydrophobic amino acids from the solvent
• and this allows the solvent to become more disordered.
• the (increasing) disorder in the universe is the sum of the order in the system (a protein) and its surroundings (the solvent): the increase in order in a protein as it folds into its #-D structure is balanced by a increase in disorder of the solvent.

Reprise:
Principle of Macromolecular Organisation.
All macromolecules are constructed by polymerization of low molecular weight units.

• Concept 1: Biopolymers are formed from monomeric units.
  • Primary structure = linear sequence of amino acids
  • All macromolecules have constant and variable regions:
  • the constant zone gives rise to regular repeating structures,
  • the variable zone, irregular and unique structures.

• Concept 2: Macromolecules have different orders of structure.
  • primary = sequence of monomers
  • secondary = local folding,eg double helix, _-helix
  • tertiary = 3D-folding of the macromolecule
  • quaternary = self association of protein subunits, each with tertiary structure

• Concept 3: The primary structure of a protein determines its higher order structure and function. This includes the secondary and tertiary structures. The correct folding into the tertiary structure is responsible for the biological function (eg, an enzyme).

• Concept 4: Macromolecules associate non-covalently to form supramolecular structures, organelles, cells.
  • quaternary structure = supramolecular assembly of 3-D structures, monomers associate into oligomers

Return to BICH 107 page Bich 107 lecture notes on proteins were last updated 09/30/03

Comments to Martyn Gunn