The document discusses proteins, their structure and classification. Proteins are made up of amino acids and have primary, secondary, tertiary and quaternary structure. Proteins are classified based on solubility and function into structural, transport, antibody, enzyme and hormone proteins.
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2 Biomolecules
The document discusses proteins, their structure and classification. Proteins are made up of amino acids and have primary, secondary, tertiary and quaternary structure. Proteins are classified based on solubility and function into structural, transport, antibody, enzyme and hormone proteins.
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• Proteins: Berzelius first coined the term in 1838 which
means ‘first order’ or prime importance.
• They are complex organic nitrogenous compounds. • Amino acids are the building blocks of proteins, they are joined together by means of a peptide bond resulting in the formation of protein. Proteins are synthesized on the ribosomes. The proteins are needed for growth and maintenance of body. The sources of protein are milk, cheese, pulses, peanuts, fish, meat etc. • The twenty amino acids are: Valine, Leucine & Isoleucine; Alanine, Arginine, Glutamine, Lysine, Aspartic acid, Glutamic Acid , Proline, Cysteine, Threonine, Methionine, Histidine, Phenylalanine, Tyrosine, Tryptophan, Asparagine, Glycine, Serine. • Phenylalanine, threonine, tryptophan, leucine, isoleucine, histidine, lysine, methionine and valine are the essential amino acids which cannot be synthesized in our body and must be taken through our diet, while non-essential amino acids can be synthesized by our body. Zwitter ion of amino acid • This is called a zwitterion. This is the form that amino acids exist in even in the solid state. If you dissolve the amino acid in water, a simple solution also contains this ion. A zwitterion is a compound with no overall electrical charge, but which contains separate parts which are positively and negatively charged. • The structure of an amino acid allows it to act as both an acid and a base. An amino acid has this ability because at a certain pH value (different for each amino acid) nearly all the amino acid molecules exist as zwitterions. One of the most useful applications of zwitterions is in SDS PAGE which is one of the most common practical procedures in molecular biology. It is a form of electrophoresis used to separate protein molecules by molecular mass • Proteins can be monomeric i.e., contain one polypeptide chain ex: lysozyme, myoglobin etc. • They can be multimeric, containing many polypeptide chains ex; Hemoglobin has 2 α and 2 β chains; Insulin has one α and one β chain. • They can also be classified as : • i) complete proteins: which have all essential and non- essential amino acids, ex: beef, animal proteins. • ii) incomplete proteins: lack some as essential amino acids, ex: plant proteins.
• A peptide bond is a chemical bond formed between two
molecules when the carboxyl group of one amino acid reacts with the amino group of the second amino acid, releasing a molecule of water (H2O). • All proteins known to exist in living beings are made of 20 amino acids. Each protein has a characteristic 3-dimensional shape, called conformation. • • 1.Primary structure: is the number and sequence of the amino acids held together by peptide bonds in a polypeptide chain. This sequence is strictly controlled by the sequences of bases in DNA. A change in the sequence creates a different protein, and the sequence of amino acids in a protein determines its function and biological activity. • 2. Secondary structure: interactions between the amino acids of the primary structure lead to folding, kinking, or even pleating of the sheets. Side by side polypeptide chains are cross- linked by hydrogen bonds. • The polypeptide chains exhibit three types of arrangement like α -helical, β -pleated sheet and random. • Linus Pauling discovered the alpha helix structure in proteins and was awarded the Nobel Prize in 1954. • In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. Ex: Keratin in hair, nails, feathers are examples of alpha helix. • In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet. The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other). Ex: silk fibroin of silk worms is an example of this. • Random: The polypeptide chain does not show geometrical order. The lack of geometry is due folding of the amino acid side chains rather than the folding of polypeptide chain. • Tertiary structure: It is the three dimensional conformation of a polypeptide. highly intricate spheres or globules are formed by the interaction of ionic, hydrogen, vander Waal’s and electrostatic interactions, disulphide bonds as well as hydrophobic interaction. Two shapes of tertiary structure are globular and fibrous. Ex: myoglobin
• Quartenary structure: Some of the proteins contain two or
more polypeptide chains called subunits. The spatial arrangement of these subunits is called quaternary structure. Ex: haemoglobin protein has 2 α and two βchains. • QUATERNARY STRUCURE OF HEMOGLOBIN Genetic Codon Table A point mutation where GAA (Glu) is replaced by GUA (Val) • Proteins are classified as fibrous and globular based on shape. • Fibrous proteins: have no tertiary structure, they are long parallel polypeptide chains and are insoluble in water, very tough and carry out structural functions, found in connective tissue, tendons, matrix of bones (collagen) in muscles, spider ‘s webs and silk worm cocoons etc. And as keratin in the hair nails, feathers and horns • Globular proteins: have complex tertiary and quartenary structures. Ex are immunoglobulins proteins, hormones and some enzymes. These proteins unlike fibrous proteins are soluble in water. • On the basis of solubility proteins are classified into: • A) Simple proteins: on hydrolysis yields only amino acids. Six types of simple proteins : • 1. Albumins: soluble in water and dilute salt solutions. Egg albumin, serum albumin from blood,β-amylase etc • 2. Globulins: insoluble or sparingly soluble in water. Soluble in dilute salt solutions. Myosin of muscles and serum globulins are examples. • 3. Glutelins: Insoluble in neutral solutions but are soluble in weak acid or basic solutions. Found in cereal grains. • 4. Prolamines: insoluble in water, but soluble in 70 to 80 percent ethanol. On hydrolysis these proteins yield proline and ammonia, ex: zein of maize, gliadin of wheat and hordein of barley. • 5. Histones: soluble in water, rich in basic amino acids like lysine and arginine, are found in cell nuclei. • 6. Protamines: rich in basic amino acids, found in nucleus associated with nucleic acids • B) Conjugated proteins: contain a non amino acid component (prosthetic group). They are six types:
• 1. Nucleoproteins: on hydrolysis yield nucleic acid plus asimple protein,
nucleic acid proteins of ribosomes and chromosomes.
• 2. Glycoproteins: contain carbohydrate as prosthetic group such as mucin
and some proteins of plasma membrane. • 3. Lipoproteins: are conjugates of lipids. Components of membranes.
• 4. Chromoproteins: chlorophyll proteins and hemoglobins. Prosthetic group
is a pigment.
• 5. Metalloproteins: many enzymes require metal as an activator ex ferritin.
• 6. Phosphoproteins : contain phosphate group linked ex is casein from milk.
• C) Derived proteins: These are derived from simple or conjugated proteins by chemical or enzymatic reaction. Examples are peptones, proteoses, and polypeptides. A proteose is any of various water-soluble compounds that are produced during digestion by the hydrolytic breakdown of proteins short of the amino acid stage. It forms after breaking down of polypeptides by gastric pepsin. In addition to proteoses, peptones are also formed at this stage. • Derived Proteins • Derived from simple or compound proteins by denaturation or some chemical reaction such as hydrolysis. • They are subdivided into Primary & Secondary derived proteins. • Primary Derived Proteins These are denatured or co-agulated proteins. Example : Egg proteins. Secondary Derived Proteins. These are intermediates formed in protein hydrolysis. Examples are : • Proteoses • Peptones • Polypeptides • Oligopeptides • Some important proteins and their functions: • Structural proteins like collagen are insoluble and serve as supporting material. Collagen forms skin, cartilage, ligaments, tendons etc, while scales of fish and reptiles and hair, feather, horns are made of keratin. • Transport proteins are carrier proteins which move molecules from one place to another around the body. Hemoglobin is one of these and is responsible for transporting oxygen through the blood via red blood cells. Cytochromes are another that operate in the electron transport chain as electron carrier proteins. • Antibodies are specialized proteins involved in defending the body from antigens (foreign invaders). They can travel through the bloodstream and are utilized by the immune system to identify and defend against bacteria, viruses, and other foreign intruders. • Enymatic proteins : act as enzymes and function in regulating biochemical reactions, ex: lipase which catalyses the hydrolysis of fats to fatty acids and glycerol. • Hormonal proteins are messenger proteins which help to coordinate certain bodily activities. Examples include insulin, oxytocin, and somatotropin. • Insulin regulates glucose metabolism by controlling the blood-sugar concentration. Oxytocin stimulates contractions during childbirth. • Contractile proteins are responsible for muscle contraction and movement. Examples of these proteins include actin and myosin. • Denaturation of proteins: In biological systems, a protein has a unique 3-D structure and a unique biological activity. This is the native form of protein. If a protein in native form is subjected to a physical change (change in temperature) or chemical change (pH change), hydrogen bonds are broken, the disturbance unfolds the protein globules and uncoils the helix of the protein molecule. The protein loses its biological activity, this is called denaturation. • The secondary and tertiary structure of the protein are destroyed but the primary structure remains same. The globular proteins are converted to fibrous proteins hence denaturation leads to coagulation, ex: coagulation of egg white when egg is boiled. • Enzymes: • Enzymes are biological catalysts which accelerate the rate of biochemical reaction, produced in living cells only. • First predicted by Berzelius in 1835, Kuhne in 1878 used the term enzyme, J.B Sumner isolated the enzyme urease in jack bean meal, Northrop isolated pepsin, trypsin and chymotrypsin. Digestion of food, absorption of appropriate molecules and production of energy all these reactions need enzymes. Enzymes are very specific for a particular reaction and they are named after the compound on which they act. • Ex : Maltase catalyses hydrolysis of maltose into glucose. Dehydrogenases remove hydrogen. • Enzymes are protein molecules of high molecular weight. Two general types of structure of enzyme molecules: • 1) Simple protein molecules : proteins containing only amino acids. • 2) Conjugated protein molecules: proteins with attached non-protein groups. It has two parts: i) apoenzyme: composed of amino acids only and ii) prosthetic group- a non protein group. The enzyme molecule consisting the protein and prosthetic group is Holoenzyme. The prosthetic group may be an inorganic cofactor or organic coenzyme. The metals known to be cofactors of enzymes are copper, iron, manganese, zinc, calcium etc. • Organic coenzymes are nicotinamide dinucleotide (NAD) coenzyme A etc. • Nearly all enzymes are proteins, although a few catalytically active RNA molecules have been identified. • Enzyme catalyzed reactions usually take place under relatively mild conditions (temperatures well below 100 oC, atmospheric pressure and neutral pH) as compared with the corresponding chemical reactions. • Enzymes are biocatalysts that increase the rate of a chemical reaction without being changed themselves in the process. • Enzymes are highly specific with respect to the substrates on which they act and the products that they form. • Enzyme activity can be regulated, varying in response to the concentration of substrates or other molecules. • They function under strict conditions of temperature and pH in the body. • Many enzymes require the presence of small, non-protein units or cofactors to carry out their particular reaction. • Cofactors may be either one or more inorganic ions, such as Zn2+ or Fe2+ or a complex organic molecule called a coenzyme. Ex Fe is required for activation of cytochrome oxidase. • A metal or coenzyme that is covalently attached to the enzyme is called a prosthetic group (heme in hemoglobin). • Some coenzymes, such as NAD+, are bound and released by the enzyme during its catalytic cycle and in effect function as co- substrates. Many coenzymes are derived from vitamin precursors. • A complete catalytically-active enzyme together with its coenzyme or metal ion is called a holoenzyme. • The protein part of the enzyme on its own without its cofactor is termed an apoenzyme. • Properties of enzymes: • 1) They are active in very small amounts. The number of moles of substrate converted per minute by one mole of enzyme is called turnover number of the enzyme. • 2) Enzymes remain unaffected by the reaction they catalyze. • 3) An enzyme hastens the completion of reaction, but it does not affect the equilibrium of the reaction. • 4) They are very specific in nature. • 5) Being proteins, they can loose their activity on heating, i.e., thermolabile. • Nomenclature and classification of enzymes: e. For example, dehydrogenases remove hydrogen atoms, proteases hydrolyze proteins, and isomerases catalyze rearrangements in configuration. • Systematic nomenclature and classification of enzymes was given by International Union of Biochemistry in 1995. Main features are: • 1) All enzymes are divided into six major classes: Viz., Oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. • Oxidoreductases catalyse oxido-reduction reactions , oxidize their substrate by addition of oxygen, removal of hydrogen or electrons. Ex: cytochrome oxidase • Transferases : transfer of a functional group such as amino, phosphate thiol group from one molecule to another. Ex: Hexokinase • Hydrolases: Catalyse the the hydrolytic cleavage of C-C, C-O, C-N, P-O bonds of their substrate by addition of water. Ex: amylase, lactase, maltase. • Lyases: Catalyse the removal of groups from their substrate. Ex: decarboxylases remove CO2 group and hydrases remove water ex: aldolase, histidine decarboxylase. C-C, C-O, C-N, and other bonds by elimination.
• Isomearses: Substrate is converted into its geometric or structural changes
within the same molecule.ex: triose phosphate isomerase, malate isomerase.
• Ligases: catalyse the linking together of compounds using ATP as energy
source. Ex: DNA ligase; pyruvate carboxylase catalyses bond between pyruvate and carbondioxide to form oxaloacetate. • The name of the enzyme has two parts, the first denotes the name of the substrate and the second ending in ‘—ase’ indicates the type of the reaction catalysed. • • . • Functions of enzymes: • Enzymes are biocatalysts, which means they speed up the rate at which reactants interact to form products in a chemical reaction. To do this, enzymes lower the activation energy required for bonds to break and new bonds to form, making the formation of a product much faster. Without enzymes, these chemical reactions would proceed at a rate that is hundreds to thousands of times slower. • Zymogens are precursors of enzymes. They are the inactive forms and become active after conversion ( for ex: cleavage by certain enzymes like trypsin converts chymotrypsinogen to is active form) . CT breaks proteins and peptides in pancreas. • Two theories • 1) Lock and key hypothesis (by Emil Fischer,1894) and Induced fit hypothesis( By D. Koshland, 1966) explain the mechanism of enzyme action. • The substance on which the enzyme acts is called substrate and the substance obtained at the end of reaction is called product. Enzymes are mostly globular proteins and have their primary, secondary, tertiary or quartenary structures. The Lock and Key hypothesis states that the enzyme and its substrate have a complementary shape, substrate binds to the active site and a complex is formed. E + S -------- ES ---------- E + P e=enzyme, S=substrate, P=product. A particular lock(substrate) can be opened by a Particular key (enzyme) • Induced Fit Hypothesis: Koshland proposed it. The active site of the enzyme does not a exist in a shape that is complementary to the substrate. Enzyme is induced to assume a complementary shape according to the substrate configuration, like a kind of ‘glove and hand relationship’. • Different enzymes show features of both models, with some complementarity and some conformational change.
• Factors affecting enzyme activity:
• Substrate concentration: If other conditions are constant, an increase in the substrate concentration increases the rate of the enzyme catalysed reaction. • Enzyme concentration: If the substrate is in excess, an increase in the enzyme concentration , increases the rate of the reaction. • Temperature: Due to their proteinaceous nature enzymes are sensitive to temperature changes and their activity is confined to a narrow temperature range. Enzymes show a temperature optimum which is between 30°C and 50°C. • pH: Most enzymes have an optimum pH range of 4 to 9. Pepsin is active at acidic pH 2.0 while trypsin is active at pH 8.2. •The substrate(s) is bound in the active site by multiple weak forces which result into the enzyme-substrate complex.
•Once bound active residues within the active site of the enzyme act on the substrate molecule to transform it first into the transition state complex and then into product, which is released.
•The enzyme is now free to bind another molecule of substrate and
begin its catalytic cycle again • The active site of an enzyme is the region that binds the substrate and converts it into product. • It is usually a relatively small part of the whole enzyme molecule and is a three-dimensional entity formed by amino acid residues that can lie far apart in the linear polypeptide chain. • The active site is often a cleft or crevice on the surface of the enzyme that forms a predominantly nonpolar environment which enhances the binding of the substrate. • The substrate(s) is bound in the active site by multiple weak forces (electrostatic interactions, hydrogen bonds, van der Waals bonds, hydrophobic interactions; and in some cases by reversible covalent bonds. • The enzymes can bind to substances other than substrate, which results in inactivation of the enzyme. These are called inhibitors and they compete with the substrate for binding to the same site on the enzyme, this can be reversed by increasing the substrate concentration. This is called competitive inhibition. • In non-competitive inhibition, the inhibitor binds to different site and cannot be reversed by increasing substrate concentration. • Isoenzymes are different forms of an enzyme which catalyze the same reaction, but which exhibit different physical or kinetic properties, such as isoelectric point, pH optimum, substrate affinity or effect of inhibitors. • Different isoenzyme forms of a given enzyme are usually derived from different genes and often occur in different tissues of the body, for example LDH-2 is present in white cells, while LDH-5 in liver and skeletal muscle. • An example of an enzyme which has different isoenzyme forms is lactate dehydrogenase (LDH) which catalyzes the reversible conversion of pyruvate into lactate in the presence of the coenzyme NADH and is used as a marker of cell damage or cell death. • LDH is a tetramer of two different types of subunits, called H and M, which have small differences in amino acid sequence. The two subunits can combine randomly with each other, forming five isoenzymes that have the compositions H4, H3M, H2M2, HM3 and M4. The five isoenzymes can be resolved electrophoretically. • Significance of Enzymes • In the absence of an enzyme, biochemical reactions hardly proceed at all, whereas in its presence the rate can be increased up to 107-fold. Thus, they are crucial for normal metabolism of living systems. The enzymes in your body help to perform very important tasks. These include building muscle, destroying toxins, and breaking down food particles during digestion
• Besides in the body, extracted and purified enzymes have many
applications. • Medical applications of enzymes include: • Enzymes are markers in various disease states such as jaundice, cancer, pacreatitis. • To treat enzyme related disorders. • To assist in metabolism • To assist in drug delivery. • To diagnose & detect diseases. • In manufacture of medicines. • Industrial applications of enzymes include: Enzymes are widely used by the food industry for processing raw materials for the production of numerous and common products such as dairy, bakery products, meat products, fruit products, beer and wine.
• Amylase, lactases, cellulases are enzymes used to break
complex sugars into simple sugars. • Pectinase like enzymes which act on hard pectin is used in fruit juice manufacture. • Lipase enzymes act on lipids to break them in fatty acids and glycerol. Lipases are used to remove stains of grease, oils, butter. • Enzymes are used in detergents and washing soaps. • Protease enzymes are used to remove stains of protein nature like blood, sweat etc. • Vitamins may be defined as a group of biomolecules, most of which cannot be produced by the body and must be supplied in small amounts in diet to perform the specific biological function for the life, growth and health of humans beings and animal organisms. • Example: Vitamin A, Vitamin K, Vitamin B etc. • Vitamins neither supply energy nor help in building tissue of the cell but their deficiency • in the body can cause serious diseases. • Plants can synthesize all Vitamins but animals can synthesize very few vitamins. Some vitamins are present in the nature also, like vitamin D which is either supplied by food or may be produced in the skin by the irradiation of ergosterol with ultraviolet light. • Human body can also synthesize some vitamin A from carotenes, some components of vitamin B complex and vitamin K are synthesized by microorganisms present in the intestinal tract. • The main sources of vitamins are our food which consists of milk, butter, green vegetables, meat, eggs etc. • Vitamins are also synthesized in the laboratory and are available in the form of tablets, capsules, which can be taken orally or as with injection as prescribed in the case of vitamin deficiency. • Classification of Vitamins • Vitamins are complex organic molecules. They are broadly classified into the following two categories: Water soluble and Fat Soluble • Water Soluble Vitamins: These vitamins are water soluble. These vitamins must be supplied regularly in diet because they are regularly excreted in urine and cannot be stored in our body. • Vitamin B1: Its chemical name is Thiamine, • Source: It is found in pulses, nut, whole cereals, rice polishing, yeast, egg yolk, milk, green vegetables and in fruits. • Deficiency Diseases: Their deficiencies cause Beriberi disease, in which legs get paralysed and cause loss of appetite. • Vitamin B2: Its chemical name is Riboflavin or Lactoflavin. Characteristics: It is sensitive to light but stable to heat. It is essential for growth and health of animals. • Sources: It is found in milk, yeast, green vegetables, meat, liver, kidney etc. • Deficiency Diseases: Its deficiency retards growth, and cause general inflammation of tongue, dermatitis and cheilosis. • Vitamin B6: Its chemical name is Pyridoxine. In fact it is a mixture of pyridoxine, pyridoxal and pyridoxamine. Source: It is found in rice bran, yeast, molasses, meat, fish etc. • Deficiency Disease: It causes specific dermatitis in rats, pellagra and anaemia in human beings, affects central nervous system, causes general weakness, convulsions, weakness, nervousness, insomnia and irritability. • Vitamin B12: Its chemical name is as cyanocobalamin. It contains cobalt. Source: It is found in milk, eggs and liver of ox, sheep, pig etc. • Deficiency Disease: It causes pernicious anaemia, inflammation of tongue and mouth. • Vitamin C: Its chemical name is Ascorbic acid.
• Characteristics: It is destroyed by cooking and prolonged exposure to air. To
avoid the loss, vegetables riches in vitamin C must be cooked in closed pan and pressure cooker. Vitamin C increases resistance of the body towards diseases, maintains healthy skin and helps cuts and abrasion to heal properly. Vitamin C, also known as ascorbic acid, is necessary for the growth, development and repair of all body tissues. It's involved in many body functions, including formation of collagen, absorption of iron, the immune system, wound healing, and the maintenance of cartilage, bones, and teeth. • For adults, the recommended daily amount for vitamin C is 65 to 90 milligrams (mg) a day, and the upper limit is 2,000 mg a day. • Source: It is found in citrus fruits, lemons, leafy vegetables, chillies, sprouted pulses and germinated grains. • Deficiency Disease: It causes scurvy, pyorrhoea. • Fat Soluble Vitamins: These vitamins are the oily substance and not readily soluble in water, however they are soluble in fat. Excess intake of these vitamins is harmful for health and may cause hypervitaminoses.
• Vitamin A: Its chemical name is Retinol. Carotenoids are precursors of vitamin A.
Vitamin A has multiple functions: it is important for growth and development, for the maintenance of the immune system, and for good vision. • Sources: It is present in milk, butter, eggs, fish liver oil, rice polishing, green vegetables etc. • Deficiency Disease: Its deficiency causes Xerophthalamia, night blindness and xerosis.
• Vitamin D: Its chemical name is ergocalciferol and commonly called Sunshine
Vitamin. It controls calcium and phosphorus metabolism. • Vitamin D is essential for several reasons, including maintaining healthy bones and teeth. It may also protect against a range of diseases and conditions, such as type 1 diabetes. • Sources: It is present in fish liver oils, butter, milk, eggs, liver and meat. Daily dose of vitamin D in human body is about 0.025 mg. • Deficiency Diseases: Its deficiency causes rickets in children and oestromalacia in adults. • Vitamin E: It is a mixture of four vitamins called α, β, ϒ, ᵟ- tocopherols. Characteristics: It is stable to heat and oxidation. • Sources: Its sources are vegetable oils (like wheat germ oil, cotton seed oil, soybean oil, peanut oil etc.), eggs, milk etc. Its daily dose to human body is about 15mg. • Vitamin E has the following functions: It is an antioxidant. This means it protects body tissue from damage caused by substances called free radicals. Free radicals can harm cells, tissues, and organs. • Deficiency Disease: Its deficiency causes sterility, increased fragility of RBCs and weakness.
• Vitamin K: Its chemical name is phylloquinone and commonly called
as Antihaemorrhagic Vitamin. And it is a mixture of two vitamins called K1 and K2. play a role in blood clotting, bone metabolism, and regulating blood calcium levels. The body needs vitamin K to produce prothrombin, a protein and clotting factor that is important in blood clotting and bone metabolism. Daily dose is 90 microgram per day for females and 120 micrograms per day for males. • Sources: Vitamin K1- alfalfa, leafy vegetables and spinach. Vitamin K2- occurs mainly in bacteria. • Deficiency Disease: Its deficiency cause haemorrhage, it lengthens the time of blood clotting