What are Proteins ?

Proteins are biological macromolecules that provide 3D structures shaped for many different individual functions. These functions include:

  • Structural Proteins: These proteins include keratins (found in hair and in the skin), the cytoskeleton and coats of viruses.
  • Enzymes: These proteins catalyse the reactions of the metabolism and the replication and transcription of DNA.
  • Antibodies: Antibodies are proteins that recognise and repel invading pathogens and inactive toxins ;
  • Regulatory Proteins: These control the transcription of genes ;
  • Sensors: Sensors detect and implement signals generated within our body and those from the environment we live in;
  • Transporters and pumps : Control the traffic into and out of cells and organelles;
  • Transducers : These are motor proteins that convert chemical to mechanical energy (e.g. for muscle contraction, kinesins and dyneins of intracellular transport, ATP synthases.

A Kinesin in action

 

Proteins: Structure and Function

 

Proteins create the structures for the wide-range of functions by varying the common underlying chemical scheme. They are linear polymers (a macromolecule composed of many repeated sub-remits) that have the same polypeptide backbone. Along the backbone is a variable sequence of side-chains that distinguishes the different proteins. The side-chain at any position is one-of-twenty canonical chemicals which make possible a common synthetic mechanism: ribosomes assemble proteins under the direction of messenger RNA (mRNA) sequences.

The three-dimensional structures of proteins are inherent in their amino acid sequences : natural proteins fold spontaneously to from individual ‘native’ structures.

The polypeptide chain is flexible, and can assume many different spatial conformations which bring into proximity different constellations of sidechains. These constellations interact with one another and with solvent (a substance that dissolves a solute). One of these conformations creates a set of stable interaction which leads to the protein’s native state at equilibrium.

The range of protein structures and functions depends on the variety in the properties of the sidechains. The 20 natural sidechains vary in size and other physiochemical properties.

  • some are polar or charged
    • they can participate in hydrogen bonding or electrostatic interactions with other residues or solvent;
  • charged atoms occur at or near ends of (relatively) long and flexible sidechains;
  • atoms close to backbone are non-polar;
  • two sidechains with positive and negative charge can form a soft bridge;
  • sidechains can be non-polar :
    • Large aliphotic sidechains are hydrophobic (do not like water);
    • The clustering of hydrophobic sidechains on the inside of proteins provides the thermodynamic force for protein-folding.

Source: Introduction to Protein Science – Arther M Lesk

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