Proteins A protein chain will have somewhere in the range of 50 to 2000 amino acid residues. This term is used because strictly speaking a peptide chain isn't made up of amino acids. When the amino acids combine together, a water molecule is lost. The peptide chain is made up from what is left after the water is lost - in other words, is made up of amino acid residues. The two simplest amino acids, glycine and alanine, would be shown as:

The general structure of an amino acid is; R could be a variety of aromatic and aliphatic groups. Amino acids can combine with each other to form dipeptides e.g. A polypeptide is made from many amino acids joining together by peptide links.

A protein chain will therefore look like this: The "R" groups come from the 20 amino acids which occur in proteins. The peptide chain is known as the backbone, and the "R" groups are known as side chains.

Primary structure of the enzyme lysozyme found in hen egg white

Secondary structure of proteins – the α- helix and β- pleated sheet. In an alpha-helix, the protein chain is coiled like a loosely-coiled spring. It is stabilised by hydrogen bonding The R groups stick out from the spiral. Each peptide group is involved in two hydrogen bonds. All the N-H groups are pointing upwards, and all the C=O groups pointing downwards. Each of them is involved in a hydrogen bond. Each complete turn of the spiral has 3.6 (approximately) amino acid residues in it.

Proline is an amino acid that does not form an alpha helix because of its cyclic structure, the structure becomes destabilised.

In a beta-pleated sheet, the chains are folded so that they lie alongside each other. The folded chains are again held together by hydrogen bonds involving exactly the same groups as in the alpha-helix. The R groups point above and below the sheet.

The Tertiary Structure. The tertiary structure of a protein is a description of the way the whole chain (including the secondary structures) folds itself into its final 3-dimensional shape. The tertiary structure of a protein is held together by interactions between the side chains - the "R" groups. There are several ways this can happen. 1) Ionic bonds between charged R groups

2) Hydrogen bonds between polar R groups

3) Van der Waals forces between non-polar molecules Several amino acids have quite large hydrocarbon groups in their side chains. A few examples are shown below. Temporary fluctuating dipoles in one of these groups could induce opposite dipoles in another group on a nearby folded chain. The forces set up would be enough to hold the folded structure together.                                                                                 

It involves the amino acid cysteine. 4) Sulphur bridges It involves the amino acid cysteine.                             If two cysteine side chains end up next to each other because of folding in the peptide chain, they can react to form a sulphur bridge.

The alpha helix are shown The beta pleated sheets are shown The disulphide bridges are shown by purple atoms bonded together. The bits of the protein chain which are just random coils and loops are shown as bits of "string".

Quaternary Structure of Proteins A protein which contains two polypeptides chains that combine. The example shown is haemoglobin

The structure of haemoglobin contains four protein chains. Two chains are called α chains and the other two are called β chains. (Not related to α helix and β pleated sheets). Haemoglobin contains such a group known as haem, which is a large, iron-containing molecule which gives haemoglobin its red colour and is responsible for binding the oxygen that haemoglobin transports round the blood stream. Each protein chain is bonded to one haem group.

The functional part of this is an iron(II) ion surrounded by a complicated molecule called haem. This is a sort of hollow ring of carbon and hydrogen atoms, at the centre of which are 4 nitrogen atoms with lone pairs on them.

Each of the lone pairs on the nitrogen can form a co-ordinate bond with the iron(II) ion - holding it at the centre of the complicated ring of atoms. The iron forms 4 co-ordinate bonds with the haem, but still has space to form two more - one above and one below the plane of the ring. The protein globin attaches to one of these positions using a lone pair on one of the nitrogens in one of its amino acids. The interesting bit is the other position.

Overall, the complex ion has a co-ordination number of 6 because the central metal ion is forming 6 co-ordinate bonds. The water molecule which is bonded to the bottom position in the diagram is easily replaced by an oxygen molecule (again via a lone pair on one of the oxygens in O2) - and this is how oxygen gets carried around the blood by the haemoglobin. When the oxygen gets to where it is needed, it breaks away from the haemoglobin which returns to the lungs to get some more. Hb + 4O2  HbO8 Heamoglobin + Oxygen  Oxyhaemoglobin

The Denaturation of proteins. This is the disruption of the protein structure which leads to temporary or often permanent loss of activity. Protein function depends absolutely on its structure.. In denaturation, the peptide bonds are not affected, but the hydrogen bonds, disulfide bonds, ionic bonds and non – polar interactions can all be disrupted. There are five ways in which denaturation can occur Mild reducing agents which can disrupt disulphide bridges Changes in pH Changes in temperature The presence of urea (a polar molecule) or other similar molecules which disrupts specific hydrogen bonds Specific metal ions which can disrupt the van der Waals forces

1) Reducing agents Reducing agents can break disulfide bonds, leading to a loss of structure. Oxidizing agents can create new disulfide bonds where they don't belong. This is the process used in hair "permanents". A reducing agent is put on the hair to break existing disulfide bonds. The hair is then arranged in a new conformation (curlers) and an oxidizing agent is added to form new disulfide bonds to maintain this new structure. 2) Change in pH When the pH of a solution containing protein is changed, the protonation state of the amino and carboxylate groups changes, and ionic bonds in the proteins will be disrupted. If the pH is outside the 3-9 range then the protein structure can be permanently destroyed.

Aspartic acid, 2-aminobutanedioic acid, residue Asp which with alkali, HOOCCH2CH(NH-)CO- + OH-          -OOCCH2CH(NH-)CO- + H2O so increase in pH (more alkaline) could disrupt a hydrogen bond involving the HOOC group, or with acid, -OOCCH2CH(NH-)CO- + H+       HOOCCH2CH(NH-)CO- so decrease in pH could disrupt an important ionic bond. The red - covalent bond connects the peptide CO/NH link of the next amino acid residue, the polypeptide linkage between two residues is NH-CO

3) Change in temperature. As temperature increases, the weakest intermolecular forces are broken first. Van der Waals forces and then hydrogen bonds are disrupted more easily than ionic bonds in the secondary, tertiary and quaternary structures of proteins. Increasing the temperature means these weak forces break up due to the extreme vibration of the secondary and tertiary structures and irreversible changes take place. Most proteins become denatured at temperatures above 60oC. 4) Presence of heavy metal ions. Eg Ag+, Hg2+ , Cd2+ These can disrupt the ionic bonds between some amino residues and can also effect the disulphide bridges between cysteine residues

Hydrolysis of proteins – breaking the peptide links. Heating proteins with concentrated hydrochloric acid breaks the peptide links and reforms the amino acids from which the primary structure is built. This is the reverse of a condensation reaction. Reflux conditions are needed for this reaction.