Proteins

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Proteins occupy ~ 50% of the cell's dry mass and contain the elements carbon, hydrogen, oxygen and nitrogen (and usually sulphur)

Proteins are composed of monomeric subunits called amino acids - there are 20 different types of amino acids


Structure of Amino Acids

  • All amino acids contain a central carbon atom which is bonded to: 
    • a hydrogen atom (H) 
    • an amine group (NH2
  • a carboxylic acid group (COOH) 
  • a variable group (R) which differs between amino acids, resulting in distinct chemical properties


Structure of an Amino Acid


Types of Proteins

There are two main classes of proteins:

  • Fibrous proteins are generally composed of long and narrow strands, which are insoluble in water and have a structural role within the cell
  • Globular proteins are generally have a more compact and rounded shape, they are soluble in water and have functional roles within the cell


Differences Between Fibrous and Globular Proteins


Functions of Proteins

Proteins are very diverse and serve a number of different roles within the cell, including:

  • Structure:  Support for body tissue (e.g. collagen, elastin, keratin)
  • Hormones:  Regulation of blood glucose (e.g. insulin, glucagon)
  • Immunity:  Bind antigens (e.g. antibodies / immunoglobulins)
  • Transport:  Oxygen transport (e.g. haemoglobin, myoglobin)
  • Movement:  Muscle contraction (e.g. actin / myosin, troponin / tropomyosin)
  • Enzymes:  Speeding up metabolic reactions (e.g. catalase, lipase, pepsin) 


Biosynthesis of Polypeptides

  • Amino acids can be joined together in a condensation reaction to form a dipeptide and water
  • This results in the formation of a peptide bond, and for this reason long chains of covalently bonded amino acids are called polypeptides
  • Proteins destined for use within the cell are synthesised at ribosomes freely located in the cytoplasm
  • Proteins destined for use outside of the cell (via secretion) are synthesised at ribosomes that are bound to the endoplasmic reticulum (i.e. rough ER)
  • Polypeptide chains can be broken down via a hydrolysis reaction, which requires water to reverse the process and cleave the peptide bond


Formation of a Dipeptide


Organisation of Proteins

Primary (1°) Structure

  • The order / sequence of the amino acids of which the protein is composed
  • Formed by covalent peptide bonds between adjacent amino acids
  • Controls all subsequent levels of structure because it determines the nature of the interactions between R groups of different amino acids


Secondary (2°) Structure

  • The way the chains of amino acids fold or turn upon themselves
  • Held together by hydrogen bonds between non-adjacent amine (N-H) and carboxylic (C-O) groups
  • May form an alpha helix, a beta-pleated sheet or a random coil
  • Secondary structure provides a level of structural stability (due to H-bond formation)


Tertiary (3°) Structure

  • The way a polypeptide folds and coils to form a complex molecular shape (e.g. 3D shape)
  • Caused by interactions between R groups; including H-bonds, disulphide bridges, ionic bonds and hydrophilic / hydrophobic interactions 
  • Tertiary structure may be important for the function of the enzyme (e.g. specificity of active site in enzymes)


Quaternary (4°) Structure

  • The interaction between multiple polypeptides or prosthetic groups that results in a single, larger, biologically active protein
  • A prosthetic group is an inorganic compound involved in protein structure or function (e.g. the heme group in haemoglobin)
  • A protein containing a prosthetic group is called a conjugated protein
  • Quaternary structure may be held together by a variety of bonds (similar to tertiary structure)
  • Not all proteins will necessarily have a quaternary structure


Levels of Protein Organisation


The Proteome

  • The totality of proteins in a cell or organism is called the proteome and the study of the way proteins function and interact is called proteomics
  • Because proteins can be modified to produce multiple functional forms, there are many more proteins than genes
  • Examples of post-translational modifications to proteins include glycosylation, phosphorylation, cleavage, etc.