2. protein structure

• Organic molecules


  Contain many carbon atoms e.g. glucose (C6H12O6)
• Inorganic molecules


  Generally do not contain many carbon atoms e.g. CO2
• Polar (hydrophilic)


  Water soluble substances. Polar substances are attracted to polar substances.
• Non-polar (hydrophobic)


  Not soluble in water. Non-polar substances are attracted to non-polar substances. Non-polar substances are repelled by polar substances.
• Hydrophilic


  Attracted to and dissolve in water
• Hydrophobic


  Attracted to and dissolve in lipids
• Monomer


  A sub-unit (e.g. amino acid) or building block of a polymer
• Polymer


  A large molecule made up of many monomers bonded together, e.g. protein
• Condensation reaction


  A reaction where two monomers join to form a larger molecule, releasing water as a by-product
• Hydrolysis reaction


  A reaction where a polymer is broken into monomers. This reaction requires the input of water.
• Function of proteins


  • Enzymes
  • Transport
  • Structural
  • Hormones
  • Receptors
  • Defence
  • Motor
  • Storage
• Proteins


  Large, complex, organic compounds. They all contain carbon, hydrogen, oxygen and nitrogen – some also contain sulfur and phosphorus. Polymers (made up of monomer units). The monomer of proteins are amino acids (20 different amino acids exist). Plants can synthesize their own amino acids, but animals depend on getting most of them from their diet. Proteins differ in numbers, types and sequences of amino acids, they may consist of thousands of amino acids.
• Amino Acids


  The monomers or subunits of proteins. Generally made of a central Carbon atom, to which are attached a Hydrogen atom, a carboxyl group (COOH), an amine group (NH2) and an R group. It is the R group in an amino acid that varies and differentiates one amino acid from another and gives the amino acid its properties.
• 1. Groups


  • Each R group has its own chemical properties, affecting how different amino acids interact with each other. Eg. Amino acids with a hydrophobic R group will likely bond with a hydrophobic amino acid (non-polar is attracted to non-polar). Negatively charged amino acids are likely to bond with positively charged amino acids.
• Protein formation


  1. Peptides: short chains of two or more amino acids bonded together (not folded)

  2. Polypeptides: long chains of many amino acids bonded together (not folded)

  3. Proteins are made of many polypeptide chains bonded together and the structure is folded. Each protein has its own specific number and sequence of amino acids.
• Polypeptide formation


  Polypeptide chains (polymers) contain a large number of amino acids bonded together by peptide bonds. They are formed in the ribosomes. The formation of peptides bonds is through condensation polymerization, a process where water is released (this reaction requires energy).
• Protein structure


  • Primary
  • Secondary
  • Tertiary
  • Quaternary
• Primary Structure (amino acid sequence)

  Specific linear sequence forming a long chain of amino acids in the polypeptide. This sequence is determined by the DNA code. Amino acids are linked together in the process of condensation polymerization. Peptide bonds between 2 adjacent amino acids form. Protein not functions at this stage.
• Secondary Structure (coiling and folding)

  • Coiling and folding of the amino acid chain due to H bonds, stabilizing its specific 3D structure. Tight coils (spirals) are alpha helices (⍺ helix). Folding forms are beta pleated sheet (β pleated sheets). Random coiling, with random sharp turns in its coils.
• Tertiary Structure


  The polypeptide folds into specific 3D shape. Composed of many secondary structures. Involves the interactions between R groups of amino acids, held together by ionic, hydrogen bonds, or disulphide bridges. Gives the protein its complex functional 3D shape. A change to just one amino acid in the primary structure may alter the folding and thus 3D shape of the protein molecule and it may not function properly. The tertiary structure determines the function of the protein. Most proteins form spherical or globular shaped molecules that are soluble in water and form a variety of functional tasks.
• Quaternary Structure


  2 or more polypeptide chains bond to form a functional protein. A variety of H bonds, ionic bonds and covalent bonds hold the polypeptide chains together and gives the overall shape to the molecule. Globular proteins eg. Haemoglobin, Fibrous protein eg. Collagen, a common animal protein.
• Conjugated Proteins


  Many proteins are molecules that consist of only amino acids. Other proteins are chains of amino acids bound with other groups of molecules, these are conjugated proteins. Eg. Nucleoproteins, found in the nucleus are comprised of both protein and nucleic acid. Eg. Haemoglobin, the four tertiary structures in the protein are bound with a Haem group (that contains Fe).
• The proteome is the complete set of proteins expressed/made by an organism. Proteomics is the study of the structure, function abundance of and interactions between the proteins in the proteome.
• Applications of proteome knowledge

  • Protein engineering: to modify, create or inhibit protein-protein interactions.
  • Medical diagnosis: all cells have a set of proteins they produce. When a protein is not produced, or it is produced at an incorrect level this information can be used as a diagnostic tool.