EP - ENGINEERING PROTEINS
Carboxylic Acids and Amines
Amino Acids and Proteins 
Protein Building
Chemical Equilibrium
Reaction Rates
Enzymes
Amino Acids and Proteins
Peptides
Proteins
Shapes of Molecules
Optical Isomerism
Amino Acids and Proteins
Amino acids are organic compounds which contain two functional groups - the basic amine group, -NH2 and the acidic
carboxyl group, -CO2H. The amino acids in proteins are mostly 
-amino acids. These are
amino acids in which both the carboxyl and amino groups are attached to the same carbon atom. The simplest example is glycine (amino
ethanoic acid):
The -carbon atom in all -amino acids except glycine is chiral and hence they form
optical isomers. The amino acids in proteins are all L-isomers.
Twenty amino acids commonly occur in proteins. The amino acids differ from each other by their side chains. Amino acids may be classified as neutral, basic or acidic, depending on how many amine and carboxyl groups they have. For example, glycine is neutral because it has one amine and one carboxyl group. Aspartic acid has two carboxyl groups, hence it is acidic. Lysine has two amine groups hence it is basic.
In a neutral solution, i.e. in water, an amino acid forms a species carrying both a negative and positive charge. This is called a zwitterion.
Peptides
Two amino acids can link together with the elimination of a water molecule to form a dipeptide. This type of reaction is called a condensation reaction. The -CONH- group which links the two amino acids together is called a peptide link.
A tripeptide contains three amino acids linked together. A polypeptide contains several amino acids linked together.
Proteins
Proteins are naturally occurring polypeptides with high relative molecular masses. These may range from 10,000 or so to several millions. The structures of proteins are very complex. It is therefore customary to consider four separate elements of protein structure. These are known as primary, secondary, tertiary and quaternary structures.
Primary Structure
This is the sequence of covalently bonded amino acid residues in the protein. Ox insulin consists of two polypeptide chains consisting of 21 and 30 amino acid residues in which the chains are linked by disulphide bridges. The number and variety of amino acids in the chain can be determined by hydrolysis to break the chain up followed by chromatography to identify the amino acids.
Secondary Structure
This is the regular folding or twisting of the polypeptide chain as a result of hydrogen bonding. A spiral structure known as a helix or a pleated sheet may result.
Tertiary Structure
This is the three-dimensional folding of the helix or sheet due to cross-linking between parts of the polypeptide chain. This cross-linking is due to bonding and interactions between the side-chains of the amino acid residues. This can take a number of forms:
- Hydrogen bonding between side chains.
- Ionic bonding. Side chain crosslinking can occur as a result of ionic bonding between anionic and cationic side chains.
- Covalent bonding. The -SH groups on neighbouring cysteine residues can be oxidised to form disulphide bridges.
Cys - S - S - Cys
- Instantaneous dipole-induced dipole attractions. This can occur between non-polar side groups, e.g. CH3.
Quaternary Structure
Some proteins, such as hæmoglobin, have a quaternary structure. The quaternary structure is composed of several sub-units. Each sub-unit is a separate polypeptide chain. The sub-units fit together in a symmetrical arrangement.
Shapes of Molecules
Electron Pair Repulsion Theory
This theory assumes that the electron pairs in the valency shells of the atoms will repel each other and try to get as far apart as possible.
In methane there are four electron pairs around the central carbon atom. These four pairs distribute themselves as far apart as possible and produce a tetrahedral shape. The angle between the bonds is 109o30'
Ammonia contains three nitrogen-hydrogen bonds each containing a pair of electrons and a lone pair of electrons on the nitrogen. As there are four pairs the spatial arrangement is approximately tetrahedral. The lone pair repels more than the bonding pairs, hence the bond angles are 107o.
Water contains two oxygen-hydrogen bonds containing a pair of electrons and two lone pairs on the oxygen. The shape is again approximately tetrahedral but the bond angle is 104.5o.
The numbers of pairs of electrons around an atom determines the shape of the molecule.
| No. of Electron Pairs | Angular Separation | Shape | Example |
|---|---|---|---|
| 2 | 180o | Linear | BeCl2 |
| 3 | 120o | Planar Triangle | BF3, BCl3 |
| 4 | 109o30' | Tetrahedral | CH4, NH4+ |
| 5 | Trigonal Bipyramid | PCl5 | |
| 6 | 90o | Octahedral | SF6 |
Optical Isomerism
If a beam of light is passed through a piece of polaroid, the emergent light vibrates in a single plane. It is said to be plane-polarised. Certain substances, either in crystalline form or in solution, have the ability to rotate the plane of polarised light. Compounds which have this property are said to be optically active. Their molecules have no centre, axis or plane of symmetry, they are asymmetric. Objects which are asymmetric are said to be chiral. The simplest type of chiral molecule is one in which four different atoms or groups are attached to the same carbon atom. It is possible to produce two optical isomers that are mirror images and are non-superimposable. The two optical isomers are called enantiomers. They have identical chemical properties and physical properties except for their effect on plane polarised light. The carbon atom to which the four different groups is attached is called the chiral centre. All amino acids except glycine have a chiral centre, hence there are two optical isomers. The proteins in our bodies are made up only from the L-enantiomer. They have the same arrangement of the four groups around the central carbon atom. You can spot them by using the 'CORN rule'. With the H atom pointing upwards, looking down on the H atom towards the carbon, the sequence CO2H, R, NH2 in a clockwise direction is the L-amino acid. The other isomer is the D-form.
