13. Examples of naturally occurring molecules from plants and animals

13a. Proteins and Amino Acids  

• Amino acids are carboxylic acids (like ethanoic acid, with the -COOH group) but one of the hydrogen atoms of the 2nd carbon atom is substituted with an amino/amine group (a nitrogen + two hydrogens gives -NH₂).
  • Another hydrogen on the same 2nd carbon can be substituted with other groups of atoms (R) to give a variety of amino acids.
  • or The simplest is aminoethanoic acid or 'Glycine'
  • and another amino acid called 2-aminopropanoic acid or 'Alanine'
• All amino acids have the general structure H₂N-CH(R)-COOH (see diagram by 5b heading).
  • R can vary, think of it as the 'Rest of the molecule!
  • R = H for Glycine, R = CH₃ for Alanine.
  • Amino acids have 2 functional groups: -COOH carboxylic acid and -NH₂ amino group.
• Amino acids can polymerise together, by condensation polymerisation, forming polypeptides.
  • The peptide linkage is formed by elimination of water between two amino acids.
  • The simplest amino acid is glycine H₂NCH₂COOH and the polymerisation can be written as ...
    • n H₂NCH₂COOH  ===>  (-NHCH₂COO-)n + nH₂O,
    • where n can be quite a large number in the polymer.
  • In general the polymerisation to form a protein or polypeptide is ...
  • HNH-CH(R)-COOH + HNH-CH(R)-COOH ==> H₂N-CH(R)-CO-HN-CH(R)-COOH + H₂O ...
  • ... to form one peptide linkage, so ...
  • n H₂N-CH(R)-COOH ==> -NH-CO-CH(R)-NH-CO-CH(R)-NH-CO-CH(R)-NH-CO-CH(R)- etc. n units long
  • ... where R is variable chemical group, as there over 20 known amino acids,
  • and so proteins are long chain polypeptides and are natural condensation polymers of amino acids.
  • Long chain polypeptides are called proteins.
  • Each polypeptide, protein, enzyme etc. has its own unique sequence of amino acids (all encoded for you in your DNA!)

Diagram showing the formation of the polyamide/polypeptide link as a water molecule is eliminated when the carboxylic acid of one amino acid, and the amino group condense together to give an polypeptide/amide link.

In this case two amino acids have a formed the simplest possible polypeptide - a simple dipeptide.

Note that at each end of the molecule, the amino/amine group (-NH₂, on left) and the carboxylic acid group (-COOH, on right) can both form a bond with another amino acid molecule by further elimination of water molecules.

So, if the process continues, as shown below), you build up a long chain polymer - known as a polyamide, polypeptide or a protein - they are all the same here.

• Proteins have the same (amide) linkages as nylon but with different units.
• Proteins are an important component of tissue structure and enzymes (powerful biological chemical catalysts) are also protein molecules.
  • Proteins tend to adopt a particular three dimensional shape (3D) which aids its function.
  • Apart from the structural proteins in you body e.g. muscle tissue, enzymes are protein molecules wrapped into a specific 3D shape to carry out their catalytic function.
  • For more detailed notes see Enzymes and Biotechnology

• When proteins are heated with aqueous hydrochloric acid or sodium hydroxide solution they are hydrolysed to amino acids.

  • see chromatography below, about how amino acids are identified in proteins.

• A spot of cooking chemistry!

  • Food is cooked for several reasons:

    • The high cooking temperature kills harmful microbes-bacteria, as long as cooked for the required time at a high enough temperature.

    • It may improves the texture.

    • It may improve the flavour and taste (but remember some foods might taste better raw e.g. lettuce!)

    • It makes it easier for the body to digest the food.

  • Degradation of protein structure

  • Most of meat from animals consists of protein together with smaller amounts of water and fat. Eggs and fish are also good sources of protein.

  • Protein molecules have a definite shape (diagram 1. above).

  • During the cooking of meat irreversible chemical changes take place.

  • The complex and specific structure of protein molecules is partly broken down in the cooking process.

  • The high cooking temperature promotes particular chemical reactions to happen.

  • The structure changes and some of the chemical bonds are broken and new molecules can be formed that have a different taste-flavour and texture giving the food its own characteristic 'cooked' character.

  • The breaking down of protein complex protein molecules is called denaturing.

  • A similar process happens in the cooking of carbohydrate foods like potatoes which are broken down into far more readily digestible molecules by breaking down the cell walls.

    • See also ...

    • Oils, fats and margarine notes

    • Aspects of food additives and cooking chemistry

13b. Chromatography - a method of amino acid analysis

• Hydrolysis means breaking down a molecule with water to form two or more products.

  • Hydrolysis is accelerated if the substance is heated with acid or alkali solutions.

• When proteins are heated with aqueous acid they are hydrolysed to amino acids.

• Acid hydrolysis of complex carbohydrates (e.g.. starch) gives simple sugars.

• (1)  (2)  (3) (4) paper chromatography

• Paper or Thin layer chromatography is used to separate coloured compounds (illustrated above).

  • (1) samples spotted onto start line, paper placed in solvent, but below start line of pencil.

  • (2) Solvent rises up paper.

  • (3) When solvent near top of paper, remove paper to dry. For colourless amino acids, you spray the paper with ninhydrin which gives a purple spot for each amino acid.

  • (4) You can then measure the Rf values to identify amino acids in the mixture.

  • To illustrate the method I've described the separation of coloured dye molecules. 1 to 5 represent five pure compounds, 6 is a mixture. Red, brown and blue make up the mixture because its spots horizontally line up with the three known colours.

    • The substances (solutes) to be analysed must dissolve in the solvent, which is called the mobile phase because it moves. The solvent may be water or an organic liquid like an alcohol (e.g. ethanol) or a hydrocarbon, so-called non-aqueous solvents.

    • The paper or thin layer of material on which the separation takes place is called the stationary or immobile phase because it doesn't move.

    • The distance a substance moves, compared to the distance the solvent front moves (top of grey area on diagram 2) is called the reference or R_f value and has a value of 0.0 (not moved - no good), to 1.0 (too soluble - no good either), but R_f ratio values between 0.1 and 0.9 can be useful for analysis and identification.

    • R_f = distance moved by dissolved substance (solute) / distance moved by solvent

• However, amino acids and sugars are colourless, but can still be separated in this way, so read on!

• Thin layer or paper chromatography can still used to separate and identify the products of hydrolysis of carbohydrates and proteins because you make them coloured by using another chemical reagent.

  • The hydrolysis can be done by boiling the carbohydrate or protein with hydrochloric acid.

  • The hydrolysed mixture is then 'spotted' onto the pencil base line of the chromatography paper.

    • Known sugars or amino acids are also spotted onto the base line too.

    • The prepared paper is then placed vertically in a suitable solvent, which rises up the paper.

  • Since the products are colourless, the dried chromatogram is treated with another chemical to produce a coloured compound.

    • Ninhydrin produces purple spots with amino acids

    • and resorcinol makes coloured spots with sugars.

  • You can then tell which amino acids made up the protein or the sugars from which the carbohydrate was formed.

    • The number of different spots tells you how many different amino acids or sugars made up the natural macromolecule.

    • Spots which horizontally match the standard known molecule spots confirm identity.

  • Starch gives one spot because only glucose is formed on hydrolysis.

    • (C₅H₁₀O₅)_n + nH₂O ===> n C₆H₁₂O₆ (where n is a very large number)

  • More on thin layer/paper chromatography.

  • Note that if organic compounds are gases or volatile (easily vapourised) liquids, they can be analysed using gas-liquid chromatography (in section 6. of the GCSE Extra Industrial Chemistry page).