PROTEINS Proteins are the most complex and most diverse group of biological compounds. If you weigh about 70 kg: About 50 of your 70 kg is water. Many and various chemicals make up the remaining 20 kg. About half of that, or 10 kg, is protein.

Proteins have an astonishing range of different functions, –Structure: e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle) –Enzymes: e.g. amylase, pepsin, catalase, etc (>10,000 others) –Transport: e.g. hemoglobin (oxygen) –Pumps: e.g. Na + K + pump in cell membranes –Hormones: e.g. insulin, glucagon

–Motors: e.g. myosin (muscle), kinesin (cilia) –Receptors: e.g. rhodopsin (light receptor in retina) –Antibodies: e.g. immunoglobulins –Blood clotting: e.g. thrombin, fibrin

Proteins are made of amino acids. Amino acids are made of four elements: C H O and Nitrogen. General structure of amino acid molecules: –a central carbon atom (called the "alpha carbon"), with four different chemical groups attached to it: -a hydrogen atom -a basic amino group -an acidic carboxyl group -a variable "R" group (or side chain)

There are 20 different R groups, and therefore 20 different amino acids. Since each R group is different, each amino acid has different properties: some are hydrophobic, some are hydrophilic, and some are ionic. The side chains interact with each other in a wide variety of ways This in turn means that proteins can have a wide range of properties

Peptide Bonds Amino acids are joined together by peptide bonds. The reaction involves the formation of a molecule of water in a dehydration synthesis reaction: Two amino acids joined together: dipeptide. Many amino acids: a polypeptide.

Carboxyl end Amino acid end

The Rules of Protein Structure The function of a protein is determined by its shape. The shape of a protein is determined by its primary structure(sequence of amino acids). The sequence of amino acids in a protein is determined by the sequence of nucleotides in the gene (DNA) encoding it.

Protein Structure Primary structure: the sequence of amino acids. (This is dictated by genes).

Secondary structure: This is the most basic level of protein folding. The secondary structure is held together by hydrogen bonds between the carboxyl groups and the amino groups in the polypeptide backbone. Because it is formed by backbone interactions it is largely independent of primary sequence The two most common secondary structures are the a-helix and the b- pleated sheet.

The  -helix. The polypeptide chain is wound round to form a helix. It is held together by hydrogen bonds running parallel with the long helical axis. There are so many hydrogen bonds that this is a very stable and strong structure

The  -sheet. The polypeptide chain zig-zags back and forward forming a sheet of antiparallel strands. Once again it is held together by hydrogen bonds.

Tertiary Structure This is the compact globular structure formed by the folding up of a whole polypeptide chain. Every protein has a unique tertiary structure, which is responsible for its properties and function. For example the shape of the active site in an enzyme is due to its tertiary structure.

The tertiary structure is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is. There are three kinds of bonds involved: –hydrogen bonds, which are weak. –ionic bonds between R-groups with positive or negative charges, which are quite strong. –sulphur bridges - covalent S-S bonds

The tertiary structure is due to side chain interactions and thus depends on the amino acid sequence.

The final three-dimensional shape of a protein can be classified as globular or fibrous. globular structure fibrous structure

Globular Proteins Globular proteins are relatively spherical in shape. Common globular proteins include egg albumin, insulin, and many enzymes They are somewhat soluble in water (depending on the sequence of amino acids) They are easily denatured

FIBROUS PROTEINS Fibrous proteins form long protein filaments with rodlike shapes. They are usually structural or storage proteins. They are generally water-insoluble and not easily denatured Fibrous proteins are usually used to construct connective tissues: tendons, bone matrix and muscle fiber.

Silk is secreted as a liquid. Those fibrous proteins solidify at contact with the air to form strong and elastic polymers.

Quaternary Structure This structure is found in proteins containing more than one polypeptide chain, and simply means how the different polypeptide chains are arranged together. Hemoglobin, the oxygen-carrying protein in red blood cells, consists of four globular subunits arranged in a tetrahedral structure.

Immunoglobulins, the proteins that make antibodies, comprise four polypeptide chains arranged in a Y- shape. The chains are held together by sulphur bridges.

PROTEIN DENATURATION Globular proteins are held in their 3D form by a variety of bonds(hydrogen bonds, ionic bonds, covalent bonds) between R-groups When these bonds are disrupted, the shape of the protein changes…it “falls apart” This usually means that is cannot accomplish its function

A number of agents can denature proteins: Changes in pH changes in salt concentration changes in temperature (higher temperatures reduce the strength of hydrogen bonds) presence of reducing agents None of these agents breaks peptide bonds, so the primary structure of a protein remains intact when it is denatured. When a protein is denatured, it loses its function.