The functions of protein are linked to their shape

Proteins are polymers of amino acids joined by strong peptide bonds. The combination of any of the twenty amino acids in any length and sequence allows an almost infinite number of possible structures and functions.

The sequence of amino acids in the polypeptide chain is termed the primary structure. The primary structure is unique to a given protein. The primary structure can fold regularly to form either an α-helix or β-pleated sheet. The secondary structure is held together by hydrogen bonds between adjacent peptide bonds. The primary structure can further fold in an irregular but not random manner to form an overall three dimensional shape that more specifically determines the biological functions of the individual protein. This 3D structure is held together by bonds formed between the R-groups of amino acids.

For movement, animals use muscle contraction. Muscle fibres are composed of two protein filaments, myosin which is a thick filament and actin which is thinner. Actomyosin cross-bridges can form between the two which move relative to one another on hydrolysis of ATP drawing actin into myosin. This sliding filament theory shows how a sarcomere contracts. This contraction is used in a variety of applications including constriction or dilation of blood vessel to modify blood flow through tissues, pupil diameter to control light entry into eyes or the generation of a force at a joint to move a hand away from a hot object.

Some proteins adopt a structural role. For example, keratin, a protein in skin, is formed from coils that twist together to form rope-like structures that are both flexible and strong. This strength is utilised in animals as claws or horns for predation or protection, or hair as camouflage or insulation. Collagen, another important structural protein that comprises connective tissue in animals, is composed of coils that are more tightly bound giving a more rigid structure.

Some proteins adopt a transport role. Channel proteins in cell membranes offer a hydrophilic passage through the hydrophobic lipid bilayer. They have a specific three dimensional shape that is complementary to the given species they transport. For example, sodium gated channels in membranes of sensory neurones allow the passage of sodium into the axon during the generation of an action potential. Similar transport proteins are carrier proteins that can change shape on binding of their transporter molecule, e.g. glucose channel in liver cells to allow glucose to pass through the membrane in preparation for the process of glycogenesis.

Proteins form a key role in the infectivity of pathogens and the immunity of the host. Proteins on the surface of pathogenic bacteria act as antigens which identify a cell as non-host. Some of these antigens can break away and act as toxins. For example, the bacteria Vibrium cholerae releases a protein toxin that opens chloride ion channels in the large intestine causing loss of chloride from epithelial cells, and loss of large volumes of water as diarrhoea and chronic dehydration. Variation in the antigenic structure brought about by mutation of the pathogen’s DNA can increase the infectivity of the pathogen as the host has no memory cells or antibodies to bind to and inactivate the antigen. Phagocytosis of pathogens eventually leads to activation of B-cells

which divide by mitosis forming clones that differentiate to form plasma cells. These cells release antibodies that are globular proteins which have variable regions that have a complementary shape to a specific antigen, allowing it to agglutinate many pathogenic particles.

A key role for proteins is to act as enzymes; biological catalysts that lower activation energy of specific reactions, allowing them to take place under controlled conditions at body temperature. They have an active site that has a specific 3D shape that is complementary shape to a specific substrate. This provides specificity to reactions. On binding, the enzyme and substrate form an enzyme-substrate complex which places strain on the bonds allowing them to break more easily. For example, the enzyme sucrase has an active site that is complementary to the disaccharide sucrose. Lactose, another disaccharide that has a similar but subtly different shape to sucrose, will not fit into this site, and is therefore not hydrolysed by the enzyme. DNA polymerase condenses adjacent DNA-nucleotides together during the formation of the phosphate-sugar backbone of DNA during semi-conservative replication. Despite being similar in structure, RNA-nucleotides require RNA-polymerase to join them during transcription. These reactions highlight the high degree of specificity elicited by the flexible nature of the primary and tertiary structures of proteins.

Chemical coordination in animals is largely brought about using protein hormones. These hormones have a tertiary structure that is complementary to that of a receptor molecule often another protein or glycoprotein positioned on the cell-surface membrane of the target cell. Examples are insulin, a protein released by β-cells of the islets of Langerhan in the pancreas during conditions of high blood sugar concentrations. The insulin travels in the blood to hepatocytes in the liver and binds to a specific membrane receptor that causes activation of phosphorylase enzyme that condense glucose into glycogen in the process of glycogenesis. Glucagon is released from α-cells in the pancreas and stimulates the hydrolysis of glycogen into glucose when blood sugar is low. Other examples of endocrine hormones include follicle stimulating hormone that matures the ova in a follicle during the follicular phase of the menstrual cycle, and luteinising hormone, that causes rupture of the follicle and the release of the ova, once it has matured.