Polypeptides may fold up to form complex 3d structures. The possible structures are broken down into 4 levels: primary, secondary, tertiary and quaternary. The primary structure of a protein is the order of the amino acids of which its polypeptides are composed. At this level, only the covalent bonds between corresponding amino acids are recognised. The secondary structure refers to the way the chain of amino acids fold or turns upon itself as a result of the hydrogen bonding (the hydrogen-oxygen attraction that holds the molecule together). There are two secondary structures- the alpha-helix and the bet-pleated sheet.
In the alpha helix a polypeptide chain is round to form a helix. It is held together by hydrogen bonds. There are so many hydrogen bonds that this is a very strong and stable structure. In the beta sheet, the polypeptide chain structure is a ‘zigzag’ like shape held by hydrogen bonds, just like the alpha sheet.
- Alpha helix Beta sheet -
The tertiary structure refers to the way a polypeptide folds and coils to form a complex molecular shape. The polypeptide may be folded and twisted at places. These cross links may occur because of the hydrogen bonding as well as sulphur bridges. The sulphur bridges are the strongest and mostly determine the shape. The quaternary structure is only present when a protein consists of 2 or more polypeptides. It refers to the way the polypeptides are arranged in the protein.
The Functions of Proteins
The functions of proteins are are related to their shapes. Proteins fall into 2 groups- globular and fibrous. In globular proteins, the polypeptide chains are tightly folded to form a curved, spherical shape. One of the most important types of proteins are enzymes, biological catalysts which control the rate of reactions (their purpose is to speed them up but they can slow reactions down as well!). The functioning of an enzyme is related to its shape more than anything. All types of proteins have unique shapes and enzymes take advantage of that. The active site of any enzyme has a unique shape in which the specific substrate molecule will fit in. The shape of the site makes sure that only the intended molecules combine with the enzyme (lock and key analogy).
Globular proteins are also important in the construction of microfilaments and microtubules (they are found in the cytoplasm and are associated with cellular movement and transport inside the cell). Microfilaments are polymers of the protein actin, whereas microtubules are the polymers of tubulin. Globular proteins are also important in buffering (changing pH for the right conditions) and antibodies are also made from them.
Fibrous proteins are insoluble and are made of long, parallel polypeptide chains. These are essential parts of many structures within the body. Keratin in found in skin and in hairs. Collagen is another fibrous protein. Its fundamental structural unit is a long 300nm, thin 1.5nm diameter protein that consists of three coiled subunits. Each chain contains exactly 1050 amino acids tied around one another in a triple helix:
All collagen molecules were thought to be made of three-stranded helical parts of similar structures so the unique properties of each type of collagen are because of segments that fold into other kinds of three-dimensional structures within the triple helix itself. The triple-helical structure of collagen is made from 3 unusual amino acids. It contains large amounts of glycine and proline (which makes up about 9% of collagen). It also contains 2 uncommon amino acids which are not inserted during the translation process in the ribosomes but afterwards with the help of enzymes – hydroxyproline, a proline with a hydroxyl group bonded to the C atom, and hydroxylysin, a lysine amino acid with a hydroxyl group bonded to it.
Each amino acid has a specific function. The side chain of glycine, a hydrogen atom, is the only one that can fit into the centre of the three-stranded helix. Hydrogen bonds linking the nitrogen-hydrogen bond of a glycine residue (a specific monomer within the protein) with a carbonyl group in a neighbouring polypeptide help to hold the three chains together and keep to the triple helix form. The fixed angle of the carbon-nitrogen peptidyl-proline or peptidyl-hydroxyproline bond allows each chain to fold into a helix with a shape such that three polypeptide chains can twist together to form the three-stranded helix.
Collagen is the main insoluble fibrous protein in connective tissue (connective tissues are mainly involved in the structure and support of living organisms) in animals and is the most abundant protein in mammals. About one quarter of all proteins in the body is collagen. It represents such a large proportion of the body proteins because it has great strength but is at the same time very flexible. It is therefore used to create tendons and ligaments. It is also responsible for the elasticity of the skin, but decreases with aging, causing wrinkles to be formed. The collagen molecules bundle together to form a long fibril structure. Collagen is found in many places throughout the body and there are more than 28 types of collagen. Over 90% of collagen, however, is either type 1, 2 or 3. Type 1 is used in the skin, tendons and bones. Type 2 is used as the main component of cartilage whereas type 3 collagen is used as the main component in reticular fibres (they form the supporting mesh for soft organs such as the liver, spleen and tonsils).
Bibliography
Advanced Biology by Roberts, Reiss and Monger, published by Nelson
http://bbc.co.uk/
http://3dchem.com/
http://wikipedia.org/
http://www.ncbi.nlm.nih.gov/