13. Naturally Occurring Molecules from plants and animals

13a. Proteins and Amino Acidsand DNA

• Amino acids are carboxylic acids (like ethanoic acid) but one of the hydrogen atoms of the 2nd carbon atom is substituted with an amino 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 can polymerise together, by condensation polymerisation, forming proteins or polypeptides.
  • The peptide linkage is formed by elimination of water between two amino acids.
  • HNH-CH(R)-COOH + HNH-CH(R)-COOH ==> H₂N-CH(R)-CO-HN-CH(R)-COOH + H₂O etc. 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
  • So proteins are condensation polymers of amino acids.
• 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.

• 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.

• DNA (deoxyribonucleic acid) are the molecules that carry the genetic code or molecular 'blueprint' for all forms of life. For example it encodes through its base components the exact sequence of amino acids needed to synthesise a particular protein.

• 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.

  • 

  • 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.

    • See also ...

    • Oils, fats and margarine notes

    • Aspects of food additives and cooking chemistry

13b. Chromatography - a method of 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)

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

• 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).

Multiple Choice Quizzes and Worksheets

KS4 Science GCSE/IGCSE m/c QUIZ on Oil Products (easier-foundation-level)

KS4 Science GCSE/IGCSE m/c QUIZ on Oil Products (harder-higher-level)

KS4 Science GCSE/IGCSE m/c QUIZ on other aspects of Organic Chemistry

and 3 linked easy Oil Products gap-fill quiz worksheets

ALSO gap-fill ('word-fill') exercises originally written for ...

... AQA GCSE Science Useful products from crude oil AND Oil, Hydrocarbons & Cracking etc.

... OCR 21st C GCSE Science Worksheet gap-fill C1.1c Air pollutants etc ...

... Edexcel 360 GCSE Science Crude Oil and its Fractional distillation etc ...

... each set are interlinked, so clicking on one of the above leads to a sequence of several quizzes

Advanced Level Organic Chemistry revision notes

Revise KS4 Science GCSE/IGCSE/O level Chemistry Revision-Information Study Notes for revising for AQA GCSE Science, Edexcel GCSE Science/IGCSE Chemistry & OCR 21stC Science, OCR Gateway Science WJEC/CBAC GCSE science-chemistry CCEA/CEA GCSE science-chemistry (and courses equal to US grades 8, 9, 10)