Proteins

• Proteins contain carbon, hydrogen, oxygen, nitrogen and sulphur.
• All amino acids have the same basic structure. Different R-groups result in different amino acids. Twenty different amino acids are commonly found in cells.
• General structure of an amino acid.

  
• A peptide bond is formed between the carboxyl group of one amino acid and the amino group of another react, also forming a molecule of water. This is a condensation reaction.
• Peptide bond.

  
• A polypeptide occurs when different R-groups are able to interact, forming different types of bond.
• The formation of a polypeptide is synthesised by the enzyme peptidyl transferase.
• The primary structure of proteins

  A linear sequence of amino acids present in a protein. Peptide bonds form between the carboxyl group of one amino acid and the amine group of the next amino acid. R-groups are not involved.
• The secondary structure of proteins

  The coiling or folding of the polypeptide chain or backbone into a 3D shape.
• Alpha helix secondary protein structure

  The polypeptide backbone forms a coil (helix), which is stabilised by the hydrogen bonds between the oxygen of a C=O and the hydrogen of a N-H.
• Beta pleated sheet secondary protein structure


  Backbone is fully extended and not coiled. Different parts of the polypeptide chain can lie parallel to each other. Stabilised by H-bonds between the O of C=O and the H of N-H.
• Tertiary structure of proteins

  The folding of the secondary structure into the final 3D shape of a protein, which also determines the function of the protein.

  Newly made polypeptide chains fold spontaneously in aqueous solutions to prevent hydrophobic R-groups from coming into contact with water. Folding brings different R-groups together, and the final shape is held by interactions between different R-groups.
• The final shape of a tertiary protein is soluble, globular proteins: hydrophilic amino acids are exposed on the outside of the protein, whereas the hydrophobic R-groups are buried on the inside away from water.
• Disulphate bonds - two molecules of sulphuric acid bonded together.
• When proteins denature, the hydrogen bonds between the amino acids break, and the protein loses its shape.
• Temperature increase breaks hydrogen bonds with kinetic energy; shape of protein unravels.
• An increase in pH prevents hydrogen bonds from being formed.
• The quaternary structure of proteins

  More than one polypeptide chain combines to form the functional protein and/or the inclusion of non-protein components (e.g. prosthetic groups).
• Globular proteins are compact, water soluble, and usually roughly spherical in shape. They prefer metabolic roles like hormones, enzymes and antibodies.
• Fibrous proteins

  Structural roles, e.g., collagen; keratin; elastin. They are unreactive, strong, and insoluble.

   
• Insulin:

  Two polypeptide chains:

  • A chain and B chain are covalently linked with disulphate bridges.

  A chain starts with an α helix.

  B chain ends with a section of β plated sheets.

  Properties:

  1. Soluble – transported in the blood plasma.
  2. Specific 3D shape – binds to specific receptors on the cell surface membrane.
• Conjugated protein – globular proteins containing a non-protein component called a prosthetic group, e.g., the haem group in haemoglobin.
• Haemoglobin

  Four polypeptide units:

  • Two α helix structures
  • Two β pleated sheets
  • Shape vital to function
  • Haem group contains Fe⁺ and is responsible for the colour.
  • Each molecule binds to four oxygen molecules.
  • Haemoglobin is a globular, conjugated with quaternary structure.
  • Red – oxygen carrying pigment found in red blood cells.
  • Each polypeptide chain has a haem group attached – one haem group per polypeptide unit.

  Haem is a prosthetic group:

  • Contains Fe⁺

  Capable of reversibly binding with a single O₂ molecule – can bind O₂ in the lungs and release it again at the cells of repairing tissue.
• Catalase (enzyme)

  Four identical subunits each with its own active site buried deep inside.

  • Fe⁺ - assists with reaction.
  • Substrate:
  • H₂O₂ is a common by-product of cellular reactions.
  • H₂O₂ can be damaging to cells if it culminates.
  • 3D shape of its active site (catalase) is complimentary to the shape of H₂O₂ molecule.
• Collagen

  Location: connective tissue found in:

  • Skin
  • Tendon ligaments
  • Nervous system
  • Wall of arteries

  Properties of collagen:

  • High tensile strength
  • Insoluble
  • Unreactive
  • Flexible
  • One collagen molecule = three polypeptides wound around each other to form a triple helix.
• Keratin

  Found in:

  • Skin
  • Nails
  • Hair

  Helical polypeptides coil around each other

  Primary sequences:

  • Lots of cystine amino acids (lots of S)

  Disulphide bonds:

  • Determines flexibility.
  • Hair less than nails
  • Elastin
• Elastin

  Many stretchy elastin molecules with covalent bonds

  Found in areas requiring elasticity, e.g.,

  • Arteries
  • Alveoli
  • Bronchioles
  • Bladder
  • Skin
  • Elastic ligament
  • Cartilage

  Properties:

  • Strong
  • Elastic
  • Insoluble

  Unreactive