Lecture 4

• Primary Structure


  Covalent interactions

  The unique, specific amino acid sequence of a protein

  Linear polymer connected by covalent peptide bonds

  Determined by genes
• Secondary Structure 


  Weak interactions

  Regular coiling or folding due to hydrogen bonding between atoms of the polypeptide backbone

  S+ and S- sections on the backbone

  Hydrogen bonds can form if these groups are in close proximity

  There are two forms of this:

  • Alpha-helix
  • Beta-strand
• Alpha-Helix (Secondary Structure)


  Forms when hydrogen bonds occur between every 4th amino acid residue within a single polypeptide strand

  Forms a coiled shape

  
• Beta-Strand (Secondary Structure)


  Shown as flat arrow pointing towards the carboxyl end

  Two or more beta-strands in either direction make a beta-sheet

  
• Tertiary Structure


  3D shape of a protein that is determined by the way it's polypeptide chain folds, primarily due to weak interactions between different parts of the chain

  Some proteins may have extra covalent bonds, such as disulfide bridges, which are particularly strong bonds and are found in proteins exposed to harsh environments
• Tertiary Structure - Weak Interactions


  Hydrogen Bonds - Form within the polypeptide chain or with water molecules

  Ionic Interactions - Occur between charged side chains and ions in solution, leading to attractions or repulsions

  Hydrophobic Interactions - Non-polar molecules tend to cluster together in water, avoiding contact with it

  Van der Waals Interactions - specifically London dispersion forces, which help stabilise the structure
• Quaternary Structure


  The conformation of an oligomeric protein (a protein consisting of two or more polypeptide sub-units

  Usually maintained by weak interactions

  Not all proteins have this structure
• Weak Interactions 


  Maintain the correct structure of biological molecules

  They allow molecules to reversibly interact

  They are of enormous importance for molecules dissolved in water such as inside and between our cells
• Weak vs Covalent Interactions

  Covalent bonds hold atoms together to form molecules

  • Discrete molecules such as H2O are held together by covalent bonds
  • Breaking a covalent bond requires a chemical reaction

  Weak interactions allow molecules and parts of molecules to interact

  • Reversible and often transient (short-lived)
  • Additive (strength in numbers)
  • Hydrogen bonds - attraction between S+ and S- forms a hydrogen bond
• Structure / Function Relationship of Macromolecules

  A molecules biological function is dependent on correct conformation (3D-shape)

  Function depends on interaction with other molecules (requires a certain shape)

  React with each other by reversible weak interactions

  Structure determines function

  • Proteins have an exact shape so that they are able to connect with an enzyme to catalyse the reaction
• Enzymeand Substrate


  Enzymes are proteins that act upon substrate molecules and decrease the activation energy necessary for a chemical reaction to occur by stabilising the transition state

  Substrates are the substance that an enzyme acts on
• How Enzymes Work

  Catalyse reactions by interacting with the substrate to make it easier for the reaction to happen (correct orientation and proximity)

  Lower the activation energy of the reaction they catalyse

  Often change conformation of molecules to aid their reaction

  Can perform the same reaction over and over again once the product is made