Proteins

• Proteins


  Polymers (and macromolecules) made of monomers called amino acids

  
• Amino acids


  The monomers of proteins

  
• There are 20 amino acids found in proteins common to all living organisms
• General structure of an amino acid

  A central carbon atom bonded to: an amine group -NH2, a carboxylic acid group -COOH, a hydrogen atom, and an R group
• Peptide bond


  Formed when a hydroxyl (-OH) is lost from the carboxylic group of one amino acid and a hydrogen atom is lost from the amine group of another amino acid, with the remaining carbon atom bonding to the nitrogen atom

  
• Dipeptides


  Formed by the condensation of two amino acids

  
• Polypeptides


  Formed by the condensation of many (3 or more) amino acids

  
• A protein may have only one polypeptide chain or it may have multiple chains interacting with each other
• During hydrolysis reactions, the addition of water breaks the peptide bonds resulting in polypeptides being broken down to amino acids

  
• Amino acids are bonded together by covalent peptide bonds to form a dipeptide in a condensation reaction

  
• Chromatography


  A technique that can be used to separate a mixture into its individual components

  
• Chromatography


  • Relies on differences in the solubility of the different chemicals (called 'solutes') within a mixture
  • Uses two phases: the mobile phase and the stationary phase
  • The components in the mixture separate as the mobile phase travels over the stationary phase
  • Differences in the solubility of each component in the mobile phase affects how far each component can travel

  
• Paper Chromatography


  The mobile phase is a liquid solvent, the stationary phase is the chromatography paper

  
• Paper chromatography method


  1. A spot of the mixture is placed on chromatography paper and left to dry

  2. The chromatography paper is then suspended in a solvent

  3. As the solvent travels up through the chromatography paper, the different components within the mixture begin to move up the paper at different speeds

  4. This causes the original mixture to separate out into different spots or bands on the chromatography paper

  
• Using chromatography to separate a mixture of Amino Acids

  • A spot of the unknown amino acid sample mixture is placed on a line at the bottom of the chromatography paper
  • Spots of known standard solutions of different amino acids are then placed on the line beside the unknown sample spot
  • Each amino acid will be more or less soluble in the mobile phase than others and will therefore separate out of the mixture travelling with the solvent at different times/distances from the line, depending on their charge and size
  • The unknown amino acid(s) can then be identified by comparing and matching them with the chromatograms of the known standard solutions of different amino acids

  
• If a spot from the amino acid sample mixture is at the same distance from the line as a spot from one the known standard solutions, then the mixture must contain this amino acid
• In order to view the spots from the different amino acids, it may be necessary to first dry the chromatography paper and then spray it with ninhydrin solution (this chemical reacts with amino acids, producing an easily visible blue-violet colour)

  
• Protein structure


  There are four levels: primary, secondary, tertiary, and quaternary
• Primary structure


  The sequence of amino acids bonded by covalent peptide bonds

  
• Secondary structure


  Occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds, forming α-helix and β-pleated sheet shapes
• Tertiary structure


  Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains), including hydrogen, disulfide, ionic, and hydrophobic interactions
• Quaternary structure


  Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule
• Each of the twenty amino acids that make up proteins has a unique R group and therefore many different interactions can occur creating a vast range of protein configurations and therefore functions
• Disulfide bonds


  Strong covalent bonds that form between two cysteine R groups, helping to stabilize proteins
• Tertiary structure


  The shape of a protein
• Bonds found within tertiary structured proteins

  • Strong covalent disulfide
  • Weak hydrophobic interactions
  • Weak hydrogen
  • Ionic
• Disulfide bonds


  Strong covalent bonds that form between two cysteine R groups
• Disulfide bonds


  • They are the strongest bonds within a protein, but occur less frequently, and help stabilise the proteins
  • They are also known as disulfide bridges
  • They can be broken by reduction
  • They are common in proteins secreted from cells e.g. insulin
• Ionic bonds


  Bonds that form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COO-) R groups
• Ionic bonds


  • They are stronger than hydrogen bonds but they are not common
  • They are broken by pH changes
• Hydrogen bonds


  Bonds that form between strongly polar R groups
• Hydrogen bonds


  • They are the weakest bonds that form but the most common as they form between a wide variety of R groups
• Hydrophobic interactions


  Interactions that form between the non-polar (hydrophobic) R groups within the interior of proteins
• Biuret test for protein

  1. Make the solution alkaline

  2. Add copper (II) sulfate solution

  3. Observe colour change to lilac/purple if protein is present
• The Biuret test is qualitative - it does not give a quantitative value as to the amount of protein present in a sample
• Globular proteins


  Compact, roughly spherical (circular) in shape and soluble in water
• Globular proteins


  • Their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings
  • Their polar hydrophilic R groups orientate themselves on the outside of the protein
  • This orientation enables them to be soluble in water
  • They play important physiological roles as they can be easily transported around organisms and be involved in metabolic reactions
  • Their specific shapes enable them to play physiological roles, for example, enzymes can catalyse specific reactions and immunoglobulins can respond to specific antigens
  • Some are conjugated proteins that contain a prosthetic group
• Fibrous proteins


  Long strands of polypeptide chains that have cross-linkages due to hydrogen bonds
• Fibrous proteins


  • They have little or no tertiary structure
  • Due to the large number of hydrophobic R groups they are insoluble in water
  • They have a limited number of amino acids with the sequence usually being highly repetitive
  • The highly repetitive sequence creates very organised structures that are strong and this along with their insolubility property, makes them very suitable for structural roles, for example, keratin that makes up hair, nails, horns and feathers and collagen which is a connective tissue found in skin, tendons and ligaments
• Differences between globular and fibrous proteins

  • Shape
  • Amino acid sequence
  • Function
  • Examples
  • Solubility