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Proteins (A2 Only)

Chemistry: AQA A Level, topic 6.7.2

Proteins

Amino acids are the monomers that form proteins. Proteins are important biological molecules with complex 3D structures.

Synthesis

Synthesis

  • Amino acids undergo condensation reactions to form proteins.
  • The carboxylic acid and amine groups can react to form a peptide linkage (biological word for amide linkage).
  • Two amino acid groups will react to form a dipeptide. Three amino acid groups will form a tripeptide and so on.
Primary structure

Primary structure

  • The primary structure is given by the sequence of amino acids.
  • The primary structure is held together by strong covalent bonds with peptide linkages happening between amino acid units.
  • In biology notation, each amino acid is represented by a three letter code. For example, alanine is Ala.
Secondary structure

Secondary structure

  • The secondary structure is a result of the arrangement of polypeptide chains which causes specific hydrogen bonding interactions and lead to a specific secondary structure.
  • There are two types of secondary structure.
  • The first is the α-helix:
  • α-Helix is a regular coiled configuration held together by hydrogen bonding. The chain twists into a coiled helix shape.
Secondary structure

Secondary structure

  • The second secondary structure is β-pleated sheets:
  • β-pleated sheets cause amino acid sequences to run parallel to one another and extend to give a structure with pleated sheets.
Tertiary structure

Tertiary structure

  • The helices and sheets in the secondary structure can fold and interact to order the polypeptide strands into the final shape of the protein.
  • The complex 3-D shape is stabilised by the following interactions of the amino acid side chains:
  • Disulfide bridges (covalent S-S bonds).
  • Weak van der Waals’ forces.
  • Hydrogen bonding.
  • Ionic bonds.

Enzymes

One of the most important functions of proteins is their use as enzymes. Enzymes are biological catalysts, which are highly specific.

Specificity

Specificity

  • Enzymes are made specific by their selective active sites.
  • They are so specific that they can even select between stereoisomers such that they will only bind to one enantiomer of a substrate.
  • An example is L-amino oxidase, which only works on the L-amino acid and not the other enantiomer, the D-amino acid.
Enzyme action

Enzyme action

  • A simple representation of enzyme action is the lock-and-key mechanism.
  • This shows a simple representation of the importance of the shape of the active site.
  • Because enzymes are proteins, this shape is determined by the 3D structure of the protein.
Drugs as inhibitors

Drugs as inhibitors

  • Enzymes can be deactivated using drugs.
  • The drug molecule can also bind to the active site.
  • The level of inhibition is dependant on:
  • The relative concentration of substrate and drugs.
  • The relative binding strength of the drug and the substrate.
Using computers to design drugs

Using computers to design drugs

  • If we know the structure of the enzyme and its active site, chemists can use computer modelling to find new drugs that would fit into the active site.
  • The modelling calculates whether or not molecules have the correct polarity and stereochemistry to fit into the active site.
  • The proposed models are then synthesised and their structure is optimised by experimental work.

Test yourself on Proteins (A2 Only)

  • What makes enzymes so selective?

  • Computers can model drugs. What two features must drugs have to "fit" into an active site?

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