7.5.1 Levels of protein structure.
7.5.2 Fibrous and globular proteins.
7.5.3 Polar and non polar amino acids in protein structures.
7.5.4 Examples of proteins.
Proteins structures are describe on four levels:
Primary Structure:
The order/ number of amino acids in a polypeptide chain.
This forms a -N-C-C-N-C-C-N-C-C- backbone to the molecules
The primary structure is read from the NH2-- terminal to the --COOH terminal.
Each amino acid is identified by its specific R group
Met-Gly-Ala-Pro is a four amino acid polypeptide beginning with Methionine-Glycine-Alanine-Proline
Most polypeptides are between 50- 1000's amino acids long. (Insulin =51, Titin= 26, 926)
There are 20 different amino acids in living things.
It is therefore possible to have an incredible diversity of primary structures. In reality on a small fraction of these polypeptides are found in living things. Indeed it is one of the revelations of molecular biology that the diversity of polypeptides within the cells of different types of organism is relatively low.
Secondary Structure:
The primary structure of a polypeptide has group projecting from the N-C-C backbone.
These groups can attract each other and through hydrogen bonding cause a folding of the amino acid chain.
There are three noted forms of secondary structure:
1. Alpha Helix:
Formed from Hydrogen Bonds
There are 3.6 amino acid residues per turn of the helix.
Notice the regular helix shape.
This is drawn as a helix that follows the -N-C-C-N-C- backbone of the polymer
Alpha helices are often the basis of fibrous polymers (see below).
The Alpha helix was first discovered by Linus Pauling.
Right handed helix.
2. Beta-pleated sheet
Beta-pleated sheets are so called because of the 'pleated' or folds when view form the side.
The polypeptide chain is much more stretched out in comparison to the alpha helix.
This Beta-pleated sheet was discovered by Pauling and Corey.
This 'sheet' often has twists that increase the strength and rigidity of the structure. (Try twisting a sheet of paper to see this effect).
3. Open Loops
Alpha helices and beta-pleated sheets are often connected together by short chains of amino acids which form neither of the previous structures but simply link other sections together (see tertiary).
These loops often connect the more recognisable helices and pleated sheets.
They are in fact often important regions of proteins including the active sites of enzymes.
Tertiary Structures:
Tertiary structure is the three-dimensional conformation of a polypeptide.
In other words there are folds in a polypeptide chain.
The polypeptide folds just after it is formed in translation.
The shape is maintained by intra-molecular bonds
Hydrogen bonds
Ionic Bonds
Disulphide Bridges
Disulphide Bridges:
Covalent bonds can form between two adjacent cysteine amino acids.
The bond is covalent.
The covalent bond stabilises the tertiary shape of a protein.
Quaternary Structure:
A number of tertiary polypeptides joined together.
Haemoglobin is a quaternary structure.
It is composed of four different polypeptide chains.
Each chain forms a tertiary structure called a haem group.
Prosthetic groups:
Proteins are often bound to inorganic groups. e.g. Haemoglobin has four polypeptide 'haem' groups each associated with and Fe2+ .
Fibrous proteins are water insoluble, long and narrow proteins.
They are associated with providing strength and support to tissues.
Collagen is the basis of the connective tissue and is composed of three left handed helices.
This is the most common protein in animals.
Keratin is another common fibrous protein which is composed of seven helices.
keratin is the major protein in hair and nail structure.
Globular proteins are near soluble (colloids).
They have more compact and rounded shapes.
They are associated with functions such as:
pigments and transport proteins( haemoglobin, myoglobin, lipoproteins)
immune system (Immunoglobulins).
There is now a more sophisticated method of describing protein structure called structural motifs.
Examples are haemoglobin and Immunoglobulin(antibodies).
Cell membrane proteins:
Those sections of the molecule that contain polar amino acids are hydrophilic and can exist in contact with water.
Polar amino acids allow the positioning of proteins on the external and internal surface of a cell membrane. Both cytoplasm and tissue fluid are water based regions.
The non-polar amino acids allow the same protein to site within the phospholipid bilayer.
The lining of the channel itself will be of polar amino acids to allow the diffusion of charged molecules and ions.
Enzymes: Polar amino acids within the active site of an enzyme allow a chemical interaction between the substrate and the enzyme to form an activated complex. This transitional state allows the weakening of internal molecular structure and therefore the reduction of the activation energy.
Hormones:
Insulin is a 51 amino acid single polypeptide.
Produced in the beta-cells of the pancreas islets.
main target tissues is muscle cells and liver cells.
Function: bring about the uptake of glucose across the cell membrane and the storage of glucose as the insoluble polymer glycogen.
Immunoglobulin:
Immunoglobulins are otherwise known as antibodies.
Produced by the plasma cells in an immune response to an infectious antigen.
Great variation exists in the heavy chains which allows a response to virtually any possible antigen surface.
Due to their high specificity in identifying antigen they are used in a wide variety of bio technologies.
Enzyme:
Enzymes reduce the energy of activation and allows a biochemical reaction to reach equilibrium more quickly.
Enzymes are large globular proteins often with prosthetic groups.
This image shows catalase which is a very large molecule.
The maximum number of substrate molecules that can be converted into product per second (excess substrate) is called the 'turn-over rate'. Liver catalase has a turnover rate of around 4x107s-1 which is quick fast!
Gas transport:
Haemoglobin molecules transport oxygen to respiring tissues.
They are contained within the erythrocytes (red cells ) of the circulatory system.
Composed of four haem groups each associated with a prosthetic Fe2+ion.
Each haem group can carry an oxygen atom.
