Biomolecule PDF

14. Biomolecule Introduction : Living organisms contain a wide variety of molecules that make up their structure and play a role in physiological processes. Proteins and cellulose are the main structural components of organisms. Through photosynthesis, plants create carbohydrates. Plants...

14. Biomolecule Introduction : Living organisms contain a wide variety of molecules that make up their structure and play a role in physiological processes. Proteins and cellulose are the main structural components of organisms. Through photosynthesis, plants create carbohydrates. Plants use minerals from their roots to make proteins. Vegetable oils and milk fats mainly consist of lipids. Organisms' genetic material is made up of nucleic acids. A biomolecule or biological molecule is defined as “A molecule produced by a living organism and essential to one or more typically biological processes.” A. Carbohydrates : It is a group of organic compounds that are made up of carbon, hydrogen, and oxygen atoms. The molecular formulae of many carbs can be expressed as Cx(H2O)y. They are found in foods and drinks in the form of sugar along with proteins and fats. Hence carbohydrates are also called saccharides. E.g. Glucose (C6H12O6 Or C6(H2O)6 Sucrose (C12H22O11 or C12(H2O)11) Starch [(C6H10O5)n or [C6(H2O)5]n] Function: Carbohydrates are a vital part of all life and are broken down in the body to release energy. Source: Plants produce carbohydrates through photosynthesis, and store solar energy in them. Classification of Carbohydrates They are classified into three broad groups in accordance with their behaviour on hydrolysis. Monosaccharide A carbohydrate that cannot be hydrolyzed further to give a simpler unit of polyhydroxy aldehyde or ketone is called a monosaccharide. Examples- glucose and fructose. Oligosaccharides Carbohydrates that yield two to ten monosaccharide units, on hydrolysis, are called oligosaccharides. Oligosaccharides further classified on the basis of no. of unit of monosaccharide. a. Disaccharide - Yield two monosaccharide units on hydrolysis. E.g. Sucrose (one glucose unit + one fructose unit), Maltose (two glucose units) b. Trisaccharide - Yield three monosaccharide units on hydrolysis. E.g. Raffinose + 2H2O Glucose + Fructose + Galactose C18H32O16 C6H12O6 C6H12O6 C6H12O6 c. Tetrasaccharide - Yield four monosaccharide units on hydrolysis. E.g. Stachyose + 3H2O Glucose + Fructose + 2Galactose C24H42O21 C6H12O6 C6H12O6 2.C6H12O6 Polysaccharides Carbohydrates that yield a large number of monosaccharide units on hydrolysis are called polysaccharides. Examples- Starch (food grains) , Cellulose (cell wall of Plant cells) and Glycogen (produced from glucose). Nomenclature of Monosaccharides : According to IUPAC system, General name for monosaccharide is glycose. If there is one aldehydic carbonyl group then it is called as “Aldose” while that with one ketonic carbonyl group then it is called as “Ketose”. These names are further modified in accordance with the total number of carbon atoms present in the monosaccharide. E.g. Glucose (C6H12O6) E.g. Fructose (C6H12O6) contain one aldehydic contain one ketonic group group hence it is an aldose hence it is an aldose with with six carbon atom six carbon atom therefore therefore name is name is aldohexose. aldohexose. Glucose : Glucose can be obtained from sucrose or starch by acid catalysed hydrolysis. Glucose occurs in nature in free as well as in combined state. a. Preparation of glucose from sucrose : Sucrose is hydrolysed by heating with dilute hydrochloric or sulphuric acid for approximately two hours. This hydrolysis transforms sucrose into a mixture of glucose and fructose. Glucose and fructose are separated by adding ethanol while cooling. As glucose is almost insoluble in alcohol, it crystallises first. The solution is filtered to get glucose crystals. b. Preparation of glucose from starch : Commercially glucose is obtained by hydrolysis of starch by boiling it with dilute sulfuric acid at 393K under 2 to 3 atm pressure. Structure and Properties of Glucose Glucose molecule contains one aldehydic, that is, formyl group and the remaining five carbons carry one hydroxyl group (-OH) each. The six carbons in glucose form one straight chain. Chemical properties of Aldohexose i.e. Glucose is Molecular formula of glucose was C6H12O6, on the basis of its elemental composition. The six carbons in glucose molecule form a straight chain. This was confirmed from the following observation Glucose gives n-hexane on prolonged heating with HI.  Glucose molecule contains one carbonyl group which is confirmed by reaction of glucose with hydroxylamine forms oxime and gives cyanohydrin on reaction with hydrogen cyanide. The carbonyl group in glucose is in the form of aldehyde. This was confirmed by reaction of glucose with bromine water (mild oxidizing agent) gets a six carbon monocarboxylic acid called gluconic acid.  Glucose contains five hydroxyl groups: Glucose reacts with five moles of acetic anhydride to form glucose penta acetate. It was further confirmed that the five hydroxyl groups are bonded to five different carbon atoms in glucose molecule. Glucose contains one primary alcoholic (- CH2OH) group : Glucose and gluconic acid both on oxidation with dilute nitric acid give the same dicarboxylic acid called saccharic acid. [O] [O] HNO3 HNO3 Optical Isomerism in Glucose : When compounds have the same molecular formula but different spatial arrangements of atoms, and are therefore non-superimposable mirror images of each other are called as optical isomers (enantiomers) and the phenomenon is called as optical isomerism. Emil Fischer, a German Nobel laureate (1902), determined the configuration of the four chiral carbons (C-2, C-3, C-4, C-5) in glucose. Glucose is an optically active molecule, with a specific rotation of +52.70. Due to its dextrorotation, glucose is also known as dextrose. The identifiers (+)-glucose and d-glucose indicate that glucose is dextrorotatory. D-glucose is a more often used term for glucose. D/L configuration system : The prefix D- or L- in the name of a compound indicates relative configuration of a stereoisomer. Simplest Carbohydrate glyceraldehyde is chosen as the standard to assign D and L configuration. Glyceraldehyde has one chiral carbon(C-2) and exists as two enantiomers. These are represented by two Fischer projection formulae The Fischer projection of (+)-glyceraldehyde shows the OH group on the right side of C-2 and is labeled as the 'D' configuration. Some way, the symbol 'L' represents the configuration of (-) glyceraldehyde.  A monosaccharide is assigned D configuration if the hydroxy group (-OH gr.) of last chiral carbon i.e. C-5 lies towards right hand side. While L-configuration is assigned if the hydroxy group (-OH gr.) of last chiral carbon i.e. C-5 lies towards left hand side. Ring Structure of Glucose : Glucose has two cyclic structures that are in balance with each other via the open chain structure. The formation of the ring structure of glucose occurs when the formyl (-CHO) group reacts with the alcoholic (-OH) group at C-5. Therefore, the ring structure is a hemiacetal structure. The only variation between the two hemiacetal structures is the arrangement of C- 1, which is a new chiral center formed by ring closure. The ∝- and β- anomers of glucose are both ring structures, with the anomeric carbon being referred to as C-1. Ring structures of glucose: Fischer projection formulae  The cyclic structure of glucose has five carbons and one oxygen in its ring. Therefore, it is a six members ring. The name pyranose structure is derived from the six-membered heterocyclic compound pyran. Thus glucose is also known as glucopyranose. The Haworth formula consider the pyranose ring as perpendicular to the plane of the paper. The under side (lowerside) of the ring is known as the ∝-side while the top side (upper side) is labeled the β-side. The α-anomer positions its anomeric hydroxyl (-OH) group (at C-1) on the α-side, while the β-anomer positions its anomeric hydroxyl (-OH) group (at C-1) on the β-side. The groups present on the right side in the Fischer projection formula appear on the α-side in the Haworth formula, and vice versa. Representation of Fructose structure Fructose is a ketohexose that rotates polarized light to the left that is it shows laevorotation with value of -92.4°. Due to the α-hydroxy keto structure, fructose is a reductive sugar. In its natural form, it is a combination of fructopyranose (main) and fructofuranose while in a combined state fructose is present in fructofuranose form. The term furanose is named in comparison to furan, a heterocyclic compound with five members. Disaccharides : Disaccharides give rise to two units of same or different monosaccharides on hydrolysis with dilute acids or specific enzymes. The two monosaccharide units are linked together by an ether oxide linkage (-O-), which is termed as glycosidic linkage. Glycosidic linkage is formed by removal of a water molecule by reaction of two hydroxyl (-OH) groups from two monosaccharide units. At least one of the two monosaccharide units must use its anomeric hydroxyl group in formation of the glycosidic linkage.  Three most common disaccharides are sucrose, maltose and lactose. a. Sucrose : Sucrose has molecular formula C12H22O11 with dextrorotation (+66.50). Hydrolysis of sucrose with dilute acid or invertase enzyme gives mixture of D-(+) glucose and D-(-) fructose. The Value of D-(-) fructose (-92.40, laevoratotion) is larger than the value of D-(+) glucose (+52.70, dextrorotation), hence the hydrolysis product is called as invert sugar with laevorotation and phenomenon is called as inversion of sucrose. Structure of sucrose contains glycosidic linkage between C-1 of ∝- glucose and C-2 of β-fructose. b. Maltose : Maltose (C12H22O11) is a disaccharide made of two units of D-glucose. The glycosidic bond in maltose is formed between C-1 of one glucose ring and C-4 of the other. Maltose gives glucose on hydrolysis with dilute acids or the enzyme maltase. The glucose ring which uses its hydroxyl group at C-1 is ∝- glucopyranose. Hence the linkage is called ∝-1,4-glycosidic linkage. The hemiacetal group at C-1 of the second ring is not involved in glycosidic linkage. Hence maltose is a reducing sugar. c. Lactose : Lactose (C12H22O11) is a disaccharide present in milk. It is formed from two monosaccharide units, namely D-galactose and D-glucose. The glycosidic linkage is formed between C-1 of β-D-galactose and C-4 of glucose. Therefore the linkage in lactose is called β-1,4-glycosidic linkage. The hemiacetal group at C-1 of the glucose unit is not involved in glycosidic linkage but is free. Hence lactose is a reducing sugar Polysaccharides : Polysaccharides are formed by linking large number of monosaccharide units by glycosidic linkages. E.g. Starch, Cellulose and Glycogen Starch is storage carbohydrate of plants and important nutrient for humans and other animals. Cellulose is the main constituent of cell wall of plant and bacterial cells. It is also main constituent of wood and cotton. Glycogen constitutes storage carbohydrate of animals and is present in liver, muscles and brain. It is also found in yeast and fungi. a. Starch : Starch is made up of multiple units of ∝-D-glucose and composed of two parts, amylose (15-20%) and amylopectin (80-85%). Amylose can dissolve in water and create a blue complex with iodine. It is made up of a chain of varying length consisting of 200-1000 α- glucose units connected by α-1,4-glycosidic linkages.  Amylopectin is water insoluble component of starch which forms blue- violet colored complex with iodine. In amylopectin, chains are formed by ∝-1,4- glycosidic linkages between ∝-glucose units, where as branches are formed by ∝-1,6- glycosidic linkages b. Cellulose : Cellulose is a straight chain polysaccharide of β-glucose units linked by β-1,4- glycosidic bonds. Hydrolysis of cellulose is carried out using concentrated strong acids at high temperature and pressure. Hence β-1,4- glycosidic bond in cellulose is very strong and difficult to hydrolyse. Enzymes present in humans can not hydrolyse this linkage. Hence cellulose cannot be digested by human beings and it serves as the fibrous content of food useful for bowel movement c. Glycogen : Glycogen and amylopectin have similar structures, but glycogen is more extensively branched. B. Proteins : Proteins are the essential building blocks that form the structure of animal bodies. Proteins in the form of enzymes play prime role in all the physiological reactions. The name protein is derived form the Greek word, ‘proteios’ which means ‘primary’ or ‘of prime importance’. Nutritional sources of proteins are milk, pulses, nuts, fish, meat, etc. Chemically proteins are polyamides which are high molecular weight polymers of the monomer units called ∝-amino acids. ∝-Amino acids : ∝-Amino acids are carboxylic acids having an amino (-NH2) group bonded to the ∝ Carbon, that is, the carbon next to the carboxyl (- COOH) group All the ∝-amino acids except glycine is chiral. ∝-amino acids obtained by hydrolysis of proteins has ‘L’ configuration. COOH COOH H2N H H2N H R H ∝-amino Acid with ∝-chiral carbon ∝-amino Acid with ∝-achiral carbon i.e. Glycine If ‘R’ contains a carboxyl (-COOH) group, then amino acid is acidic amino acid. If ‘R’ contains an amino (1°, 2°, 3°)group, then amino acid is basic amino acid. The other amino acids having neutral or no functional group in ‘R’ are called neutral amino acids.  ∝-Amino acids have trivial or simple names and are usually represented by three letter symbols or one letter symbol. There are total 20 amino acids which is commonly found in protein. Out of these 10 amino acids can not synthesized in human body and obtained theough diet are called as essential amino acid. E.g. Phenylalanine, Valine, Tryptophan, threonine, Isoleucine, Methionine, histidine, Leucine, Threonine and lysine ∝-Amino acids are water-soluble crystalline solids with a high melting point. An ∝- amino acid molecule consists of both acidic carboxyl (-COOH) and basic amino (- NH2) groups. Proton transfer from the acidic group to the basic group of an amino acid produces a salt, which is a dipolar ion known as the zwitter ion.  E.g. zwitter ion and the other forms of alanine. Peptide bond and Protein : Proteins are break down into peptides in stomach and duodenum due to pepsin and trypsin enzymes. Polypeptides are further broken down to ∝-amino acids. This means that proteins are produced by linking ∝-amino acids together. The bond between ∝- amino acids is known as a peptide bond. E.g. When carboxyl group of glycine and amino group of alanine combine, result in the formation of dipeptide called as glycylalanine with elimination of water molecule. O H O H2N CH2 C + N CH C -H2O OH H CH3 OH Glycine Alanine  Combination of a third molecule of an ∝-amino acid with a dipeptide would result in formation of a tripeptide. Similarly linking of four, five or six ∝-amino acids results in formation of tetrapeptide, pentapeptide or hexapeptide respectively. Polypeptides are formed when ten or more ∝-amino acids are joined together by peptide bonds. The -CHR- units connected by peptide bonds are known as 'amino acid residues'. The two ends of a polypeptide chain of protein are not identical. The end having free carboxyl group is called C-terminal while the other end having free amino group is called N-terminal. In the dipeptide glycylalanine glycine residue is N-terminal and alanine residue is C-terminal. N-terminal O CH3 C-terminal H2N CH2 C NH CH COOH Glycylalanine Types of Proteins : Proteins are classified into two types on the basis of molecular shapes a. Globular proteins : The molecules of globular proteins are spherical. This form is the result of coiling around the polypeptide chain of protein. They are water soluble. E.g. Insulin, Egg albumin, Serum Albumin, Legumelin b. Fibrous proteins : The molecules of fibrous proteins are elongated, rod like shape. This form is the result holding the polypeptide chains of protein parallel to each other. They are water insoluble. E.g. keratin (present in hair, nail, wool), myosin (protein of muscles). Structure of Proteins : The shapes of protein molecules are the result of four level structure of proteins. a. Primary structure of proteins : The sequence consists of ∝-amino acid residues connected by peptide bonds. The primary structure of proteins is represented by writing the three letter symbols of amino acid residues in the order they occur in the protein. The symbols are separated with dashes. The left end shows the N-terminal amino acid residue, while the right end shows the C- terminal amino acid residue. a. Representation by structural formula b. Representation with amino acid symbols b. Secondary structure of proteins : The three-dimensional organization of localized portions of a protein chain is known as the secondary structure of proteins. The secondary structure is formed by hydrogen bonding between one amide linkage's N-H proton and another's C=O oxygen. Two types of secondary structures commonly found in proteins are ∝-helix and β-pleated sheet. ∝-Helix : The ∝-helix forms when a polypeptide chain twists into a right handed or clockwise spiral. Characteristic features of ∝-helical structure are The helix has 3.6 amino acids per turn. A C=O group of one amino acid forms hydrogen bond with N-H group of the fourth amino acid along the chain. Hydrogen bonds run along to the helix's axis, whereas R groups extend outward from the core. E.g. Myosin in muscle and ∝-keratin in hair β-Pleated sheet: When two or more polypeptide chains, called strands, line up side-by-side then secondary structure is called as β-pleated sheet. Characteristic features of β-pleated sheet structure are: The C=O and N-H bonds are located in the plane of the sheet. The N-H and C=O groups of close amino acid residues in neighboring chains form hydrogen bonds. The R groups are oriented above and below the plane of the sheet Proteins typically contain ∝-helix and β-pleated sheet sections, as well as random areas that do not fit into any of these structures. For example: Spider dragline silk protein is strong due to β-pleated sheet region, yet elastic due to ∝-helical regions in it. c. Tertiary structure of proteins: The three-dimensional shape adopted by the entire polypeptide chain of a protein is called its tertiary structure. It is the result of folding of the chain in a particular manner that the structure is itself stabilized and also has attractive interaction with the aqueous environment of the cell. Hydrogen bonding, dipole-dipole attraction (due to polar bonds), electrostatic attraction (due to ionic groups such as -COO- and NH3+ on the side chain), and London dispersion force are all forces that stabilize a specific tertiary structure. Oxidation of nearby -SH groups (in cysteine residues) forms disulfide bonds (-S-S-) also stabilize the tertiary structure d. Quaternary Structure of Proteins: When two or more polypeptide chains with folded tertiary structures come together into one protein complex, the resulting shape is called quaternary structure of the protein. Each individual polypeptide chain is called a subunit of the overall protein. E.g. Hemoglobin (Hb) consists of four subunits called haeme held together by intermolecular forces. It can transport oxygen only when all the four subunits are together. Denaturation of proteins It is the process by which the molecular shape of protein changes without breaking the amide/peptide bonds that form the primary structure. Denaturation results in disturbing the secondary, tertiary or quaternary structure of protein. This causes change in properties of protein and the biological activity is often lost. E.g. Globular proteins are typically folded with hydrophobic side chains. Denaturation exposes the hydrophobic region of globular proteins and make them water soluble. Enzymes : Various chemical reactions take place in human or animal bodies at pH of 7.4 and temperature of 37°C with the help of biological catalyst called as Enzymes. E.g. Insulin (hormone) secreted by pancreas to controls blood sugar level amylase (enzyme) present in saliva which hydrolyzes starch Enzyme catalysis is highly specific. E.g. Mineral acid can catalyzes hydrolysis of many types of compounds such as esters, acetals and amides but enzyme who can catalyzes hydrolysis of amide will not work on ester or acetals. Mechanism of Enzyme Catalysis An enzyme contains an active site on its surface where substrate molecule can only connect to this active site if it has appropriate size and shape. Once in the active site, the substrate is retained in the proper orientation for reaction and the products are formed. The products leave the active site and the enzyme is then ready to act as catalyst again. This mechanism is called as lock-and-key mechanism. Some enzymes are so efficient that they can catalyzes the reaction of 1000 substrate molecule in 1 seconds. Industrial application of enzyme catalysis Conversion of glucose to sweet-tasting fructose, using glucose isomerase Manufacture of new antibiotics, using pencillin G acylase Manufacture of laundry detergents, using proteases Manufacture of esters used in cosmetics, using genetically engineered enzyme C. Nucleic Acid : Nucleic acids are naturally occurring chemical compounds that serve as the primary information-carrying molecules in cells. This information is called as genetic information. Also they play an important role in directing protein synthesis. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). RNA are found mainly in the fluid of living cells (cytoplasm) while DNA are found primarily in the nuclei of living cells. Nucleic acids are large, complex molecules called as nucleotides, which are the repeating units of the molecule. Each nucleotide is made up of a five-carbon sugar, a phosphate group, and a nitrogenous base.  The structural aspects of nucleic acids are as follows 1. Nucleotides : Nucleic acids are unbranched polymers of repeating monomers called nucleotides. In short, they have a polynucleotide structure. DNA molecules contain several million nucleotides while RNA molecules contain a few thousand nucleotides. Single nucleotide (monomer) contain a monosaccharide, a nitrogen containing base and a phosphate group. In RNA, the sugar component of nucleotide unit is D-ribose, while in DNA, it is 2- deoxy-D-ribose. D-ribose (present in RNA) 2-deoxy-D-ribose (present in DNA)  Nucleic acids contain total five nitrogen-containing bases. Three bases with one ring (cytosine, uracil and thymine) are derived from the parent compound pyrimidine. Two bases with two rings (adenine and guanine) are derived from the parent compound purine. Uracil (U) occurs only in RNA while thymine (T) occurs only in DNA.  A nucleoside is formed by joining the anomeric carbon of the furanose with nitrogen of a base. While numbering the atoms in a nucleoside, primes (') are used for furanose numbering to distinguish them from the atoms of the base RNA nucleoside DNA nucleoside  Nucleotides are formed by adding a phosphate group to the 5'-OH of a nucleoside. Thus, nucleotides are monophosphates of nucleosides. Some nucleotides have abbreviated names such as AMP, dAMP, UMP, and dTMP. The first capital letter is derived from its corresponding base. MP stands for monophosphate. The small letter 'd' at the beginning signifies deoxyribose in the nucleotide. Structure of Nucleic Acids Nucleic acids (DNA and RNA) are polymers of nucleotides, formed by joining the 3' – OH group of one nucleotide with 5'-phosphate of another nucleotide. Two ends of polynucleotide chain are distinct from each other. One end having free phosphate group at 5' position is called 5' end. The other end is 3' end and has free OH- group at 3' position.  The nucleotide sequence is the main structure of nucleic acids Different nucleic acids have distinct primary structure. It is the sequence of bases in DNA which carries the genetic information of the organism. The polynucleotide chains of nucleic acids are termed after the base sequence, which begins at the 5' end and uses the base's one-letter symbol. E.g. Name CATG means there are 4 nucleotides containing the base cytosine, adenine, thymine and guanine in the indicated order which is start form 5' end. DNA double helix : In 1953, James Watson and Francis Crick proposed a double helix model for DNA structure, which was then confirmed using electron microscopy. Salient features of the Watson and Crick model of DNA are: DNA is made up of two polynucleotide strands that twist together to form a right-handed double helix. The two strands run in opposite directions; one from the 5' end to the 3' end, while the other from the 3' end to the 5' end. The sugar- phosphate backbone lies on the outside of the helix and the bases lie on the inside, perpendicular to the axis of the helix. The double helix is stabilized by hydrogen bonding between the bases of the two DNA strands. This gives rise to a ladder like structure. Adenine always forms two hydrogen bonds with thymine, and guanine forms three hydrogen bonds with cytosine. Thus A - T and C - G are complementary base pairs. It may be noted that RNA exists as single stranded structure. Fig. Hydrogen bonding between complementary base pairs Fig. DNA double helix