Biological Molecules: Structure and Function - PDF

# BIOLOGICAL MOLECULES ### Major Concept In this Unit you will learn: * Introduction of Biological Molecules * Importance of water molecules * Carbohydrates * Proteins * Lipids * Nucleic acids * Conjugated molecules ### Introduction Biochemistry: The branch of biology which explains...

# BIOLOGICAL MOLECULES ### Major Concept In this Unit you will learn: * Introduction of Biological Molecules * Importance of water molecules * Carbohydrates * Proteins * Lipids * Nucleic acids * Conjugated molecules ### Introduction Biochemistry: The branch of biology which explains the biochemical basis of life is called Biochemistry. It is one of the most important branch of biology due some reasons given below: * It provides information about all the processes carried out in the living organisms from construction of body structures to flow of information from nucleus, especially DNA for enzyme/ protein synthesis and control of all the mechanisms. * It provides information about abnormal mechanisms which lead to diseases. It ultimately open doors to the development of medicines and medical equipment to elucidate these abnormalities. * The recent concept and technologies of biochemistry enabled us to investigate and understand most challenging and fundamental problems of biology and medicine e.g. how does cells find each other to form a complex organ? How does the growth of cells controlled? What are the causes of cancer? What is the mechanism of memory? Biochemistry is the only branch of science which answer these questions properly. As we know. that organisms are made up to tissues and cells while cells are made up of molecules, molecules are chemically bonded atoms. It means that fundamentally living things or organisms are made up to chemicals which explains the second postulate of cell theory i.e. structure and function of cell are dependent upon their chemical composition. Therefore it is necessary to study the chemical composition of cell and reactions which carry down in these cells to understand the different structures and metabolisms of an organism. ## 1.1 CHEMICAL COMPOSITION OF CELL: It is already established that all living organisms are structurally composed of cells and living cell contains a living matter called Protoplasm. The actual chemical composition of protoplasm is still not known perfectly. However, chemically it contains 70% to 90% of $H_2O$. If the water is evaporated, the remaining mass of cell is called Dry Weight of cell, consist of many carbon containing long chain molecules called Biomolecules which are the types of organic molecules. So, the compounds produced by living organisms are called biomolecules. The elements which are involved in the synthesis of biomolecules are mainly six i.e. carbon, hydrogen, oxygen, nitrogen, phosphorus and sulphur. The form approximately 98% of the biomolecules. ## 1.1.2 Fundamental types of Biomolecules: Biomolecules can be divided into following groups according to variability in their structures and functions in cells and organisms i.e. 1. Carbohydrates 2. Proteins 3. Lipids 4. Nucleic Acids 5. Conjugated Molecules **Table 1.1 Biomolecules their units and linkages** | Biomolecules | Units | Linkages | | :------------------------------ | :-------------------------------- | :--------------------- | | Carbohydrates (oligo & Polysaccharide) | Monosaccharides | Glycoside linkage | | Proteins | Amino Acids | Peptide linkage | | Lipids | | | | Fats & Oils | Glycerol & Fatty Acids | Ester linkages | | Phospholipids | Glycerol, Fatty acids, Phosphate & Choline. | Ester & c-c linkages | | Terpenoids | Isoprenoids units | c-c linkages | | Nucleic Acids | | | | DNA | Deoxyribonucleotides | Phosphoester linkages | | RNA | Ribonucleotides | Phosphoester linkages | | Conjugated molecules | Different biomolecules | Different linkages | There is a variation found in literature about the percentage of biomolecules present in the cell. It is because, different cells within the same body have different amount of biomolecules. Therefore, these values are always taken as average values. Approximate percentage of chemical composition of a typical bacterial and a typical mammalian cell is given in table 1.2. **Table 1.2 Chemical compositions of cells (in %)** | Molecules | Bacterial Cell | Mammalian Cell | | :--------------------- | :------------- | :------------- | | Water | 70 | 70 | | Protein | 15 | 18 | | Carbohydrates | 3 | 4 | | Lipids | 2 | 3 | | DNA | 1 | 0.25 | | RNA | 6 | 1.10 | | Other Organic Compounds | 2 | 2 | | Inorganic Ions | 1 | 1 | ## 1.1.3 Synthesis and Breakdown of macromolecules (Polymers): ### (a) Synthesis of macromolecules (polymers) by Condensation: Molecules which form the structure and carry out activities of the cells are large in size and highly organized molecules called macromolecules which are made up of large numbers of low molecular weight, small molecules the subunits called monomers or building block. Therefore the macromolecules are also called polymers (poly = many, mers = parts). Biomolecules which are mentioned above are all macromolecules or polymers. Macromolecules are constructed from monomers by a process that resembles coupling of rail cars onto a train. The basic structure of each group of macromolecule is very similar in all organisms from bacteria to human beings. In this process monomers are joined together by removing -OH from one monomer and ⁺H from another monomer so both monomers form a new covalent bond between them, this process of joining two monomers by removing water molecule is called condensation or dehydration synthesis. Condensation always takes place by proper enzymes and energy expense. ### (b) Break down of macromolecule by hydrolysis: Process where macromolecule (polymer) are broken down into their subunits (monomers) by addition of $H_2O$molecule is called hydrolysis. It is just revers of condensation, during this process a water molecule breaks into H+ and OH ions with the help of enzyme, whereas OH group to one monomer and H attaches to the other by breaking linkage bond between two monomers. During this bond breaking energy is released and made available for other metabolic processes. During metabolism, macromolecules are either formed or broken down in the cell, when cell rebuild many of its structures. In heterotrophs, during digestion macromolecules broken into monomers by hydrolysis with the help of hydrolytic enzymes, these monomers when reach to cell again form macromolecules by the process of condensation. In autotrophs, cell produce monomers from inorganic molecules like $CO_2$, $H_2O$, $NO_3^{-1}$, $SO_4^{-2}$etc. These monomers latter on assembled to form macromolecules in source or sink tissues by the process of condensation, while the other cell when require these molecules either for building purpose or to produce energy, these molecules break into monomers by the process of hydrolysis. ## 1.2 IMPORTANCE OF WATER: Water is the most abundant component in living cell. Its amount varies approximately from 70% to 90%. It is the medium of life. Almost all reactions of a cell occur in the presence of water. It also takes part in many biochemical reactions such as hydrolysis, also provides raw material for photosynthesis. The ability of water to play its wide variety of roles and the reasons for its importance in biological systems is due to the chemistry of $H_2O$ molecule. The chemical formula of water is $H_2O$, which means that the two atoms of hydrogen are joined to one atom of oxygen. Water is a polar molecule. It means that it has partial negative charge (δ¯) on oxygen and partial positive charge (6+) on hydrogen atoms due to difference in electronegativities of hydrogen and oxygen atoms. This separation of electrical charges is called Dipole, which give the water molecule very important properties i.e. high polarity, formation of hydrogen bond, cohesion, adhesion, high specific heat, high heat of vaporization, hydrophobic exclusion, ionization and low density of ice. These properties make it best solvent and cradle of life. ### 1.2.1 Hydrogen bond: It is an intermolecular force of attraction formed between two molecule one of which contain partially charge $𝐻^+$ and other contain partial$𝑂^−$ charge as present in water. These charges attract two molecules, this force of attraction due to $𝐻^+$and $𝑂^−$ is called Hydrogen bond. Due to this Hydrogen bonding two molecules have following two types of characters. ### (a) Cohesion or Cohesive force of attraction: The attractive force between similar molecules is called cohesive force of attraction. Due to polar nature water molecules attract each other and form H-bonds between them to form a long chain of water molecule, which help it in flowing freely. It flows as protoplasm in cell, as blood in blood vessels, as transporting fluid in the conducting tissues of plants. ### (b) Adhesive force of attraction or Adhesion: The attractive force between dissimilar molecules is called Adhesive force of attraction. Due to polar nature, water molecule attracts other charged molecules and attached with them. It can hold the water molecules in the vessels and prevent them from backward flow. ### 1.2.2 High specific heat: Specific heat of a substance is the amount of heat energy required to raise the temperature of 1gm of that substance by 1C° (e.g. 15C° to 160°). The specific heat of water is high due to its polar nature and hydrogen bonding between their molecules. It means water required high amount of heat to make changes in its temperature or warm up. It works as temperature stabilizer for organism and hence protect protoplasm against sudden thermal charges. ### 1.2.3 High heat of vaporization: The amount of heat required to change liquid state of water to vapor state is called heat of vaporization. Greater the heat of vaporization higher will be the chances of stability in state or vice versa. Water has very high heat of vaporization i.e. 574 kcal/kg, therefore water requires to absorb high heat to change its state from liquid to vapors. It gives stability to water molecules and its state in cell. It plays an important role in thermoregulation. It also provides cooling effect when evaporate during transpiration are perspiration. ### 1.2.4 Hydrophobic exclusion: It is the tendency of water to coalesce oil drop into large droplet. The by the presence of hydrophobic oil and form new bonds. The water molecules then form more hydrogen bonds with themselves and the nonpolar molecules clump together. This ### 1.2.5 Ionization of water: The water molecules ionize into 𝐻+ and 𝑂𝐻°. This reaction is reversible and also maintain equilibrium. Due to ionization property water may behave as acid or base .i.e. Amphoteric in nature. It also behaves asbuffer due to this nature. It maintains pH for enzymatic activities in cells and organs. ### 1.2.6 Anomalous behavior of water: Water shows different behavior below 4°C. Usually matter contract at low temperature but due to hydrogen bond below 4°C, water expands which decreases its density so at 0°C water expands maximally in ice condition. The low density water in ice become lighter, comes above the surface of high density water of liquid. It makes the life possible under frozen water. ## 1.3 CARBOHYDRATE (CARBO = CARBON, HYDRATE = WATER): The literal meaning of word carbohydrate is hydrated carbon i.e. water containing carbon. Thus biomolecule contain C, H and O as element where the hydrogen and oxygen are present in the simple ration of 2:1 as present in water. The general formula of carbohydrate molecules is $C_nH_{2n}O_n$, whereas 'n' is the whole number. According to I.U.P.A.C carbohydrates are defined as "the polyhydroxy carbonyl compounds”, carbonyls are aldehydes or Ketones. Main source of carbohydrates are plants because they synthesize carbohydrate molecules as primary product during photosynthesis, other bio-molecules are produced from carbohydrate during different metabolic pathways. They are sweet in taste if feels therefore called sacchrum or Saccharide. They are also called sugars. Carbohydrate found abundantly in all organism, like cellulose in cell wall of plant, paper, starch is stored in cereal grains, tubers, sugar cane, etc. It plays both structural and functional role. ### 1.3.1 Classification of Carbohydrates As we have discussed earlier that carbohydrate molecules are also called 'Saccharides' these Saccharides are classified into three group. (i) Monosaccharide (ii) Oligosaccharide (iii) Polysaccharide (i) Monosaccharide: (Mono = one; Saccharide = Sugar) The group of carbohydrate molecules which contain only one sugar molecule. They cannot hydrolyses due to this reason. The empirical formula of their molecules is $C_nH_{2n}O_n$ e.g. Ribose ($C_5H_{10}O_5$). Fructose $C_6H_{12}O_6$, etc all are found in white crystalline solid with sweet taste and soluble in water. Monosaccharide can further classified on the basis of C atoms present in them, the suffix ‘Ose' use with no: of C atoms present in them as given in following table. **Table 1.3 Classification of monosaccharides** | Class | Formula | Example | | :------- | :-------- | :------------------------------------------------------ | | Triose | $C_3H_6O_3$ | Glycerose (Glyceraldehyde) Dihydroxy acetone etc. | | Tetrose | $C_4H_8O_4$ | Erythrose, Erythrulose etc. | | Pentose | $C_5H_{10}O_5$ | Ribose, Ribulose etc | | Hexose | $C_6H_{12}O_6$ | Glucose, Fructose, Galactose etc | | Heptose | $C_7H_{14}O_7$ | Glucoheptose. | Glycerose and Dihydroxy acetone are important triose, produced during respiration. Tetrose are rare in nature, it occurs in some bacteria, pentose sugar form basic skeleton of nucleic acid. Hexose are most important sugars from biological point of view. Glucose found in ripe fruit, sweet corn and honey. It is also found in all known polysaccharide in combined state. Fructose another hexose present in fruit so called fruit sugar usually they are found in ring structures but we can also draw their structure in open chain form: The hexose are further divided into aldohexose isomers (having same molecular formula but different structural formula) like glucose, galactose, mannos etc and ketohexose isomers like fructose, sorbose, psicose etc. ### (ii) Oligosaccharides: The type of carbohydrate which are made up to 2 to 10 monosaccharides. These are comparatively less sweet in taste and less soluble in water. They can hydrolyze. The most common type is disaccharide, on hydrolysis yield two monosaccharides. The covalent bond between these two monosaccharides is Glycosidic bond or linkage. A glycoside is simply a ring shaped sugar molecule that. is attach to another molecule, the sugar ring may be either 5 membered ring or a six membered ring. For example sucrose is a disaccharide, composed of two sugar units a glucose and a fructose. The disaccharide may be reducing or non-reducing sugar. The reducing sugar is any carbohydrate which is capable of being oxidized and causes the reduction of other substances without hydrolysis. It is due to the presence of free aldehyde or free ketone group. Examples are maltose, lactose etc. The non-reducing sugars are carbohydrate which are unable to be oxidized and do not reduce other substance. It is due to absence of free aldehyde or ketone groups, e.g. sucrose or refinose etc. Living organisms especially plants transport their sugar from source (leaf) to sink (fruit) tissues in the form of non-reducing sugar where glycosidic bonds are formed between ‘carbonyl' groups of both sugars. Sucrose is the sugar which is non-reducing. It contains more energy i.e, it is energy efficient in transport and storage. During transport it is not oxidized and react with other substance so no intermediate reaction with other molecules occur. ### (iii) Polysaccharide: These are high molecular weight carbohydrates which on hydrolysis yield many monosaccharides. These are formed by the condensation, hundreds or thousands of Monosaccharide units, e.g. starch, glycogen cellulose and chitin. ### 1.3.2 Starch: It is the most important and abundant reserve food material of higher plants, found in cereals, legumes, tubers and other vegetables. It is made up of many glucose molecules joined together in straight chain amylose which and a branched chain amylopectin, which insoluble in hot and cold water. It gives blue color to iodine. ### 1.3.3 Glycogen : It is also a polymer of glucose. Its molecular structure is similar starch but found in animal therefore it is commonly called animal starch is mainly found in bacteria, fungi, in animals abundantly found in liver and muscles. It gives red color with Iodine. ### 1.3.4 Cellulose: It is also a polymer of glucose, most abundant carbohydrate found in nature. It is highly insoluble in water. It is not digested in human body. In cellulose the glucose units are joined in straight chain and no branch chain present in it. This straight chain become spirally coiled and condensed to form tubes. These tubes of cellulose form cell-wall of plant cells. Cellulose give no colour to iodine. ### 1.3.5 Chitin ($C_8H_{13}O_5N_n$): It is a long chain polymer of N-acetyl glucosamine, an amide derivative of glucose. The structure of chitin is similar to cellulose, forming crystalline Nano fibrils. Functionally, it is comparable to Keratin protein. Chitin is modified polysaccharide contains Nitrogen which allows for increased hydrogen bonding between adjacent polymers, giving it more strength. In its pure and unmodified form chitin is translucent, pliable, resilient and quite tough in most arthropods but it is mostly found in modified form such as proteineceous matrix form exoskeleton of insects, with$CaCO_3$ in the shells of mollusks and crustaceans, composite material is much harder and stiffer than pure chitin. Stereoisomers in Carbohydrates and its role in artificial sweetness: Many sugar molecules have stereoisomers i.e. the molecules are mirror images of each other. Most of the sugars in our body are right handed. The taste of right handed and left handed sugars are same, protein (Enzymes) are also right handed and left handed. The enzymes which are present in our body are also right handed therefore right handed enzymes metabolize right handed sugars only. They are unable to digest or metabolize left handed sugars. The artificial sweetener which are used by diabetic patients usually are left handed sugars, these sugars have same mass and same sweetens but have zero calories. These sugars are not digested in our body because all of our enzymes are right handed and they are specific to break down the right handed sugars. The left handed won't fit into catalytic site consequently there will be no breakdown of these sugar, no metabolism and no calories. ## 1.4 PROTEIN: (GR: PROTEIOS MEANS 'FIRST RANK') Proteins can be defined as the polymers of specific amino acid arrange in a particular manner which perform definite function. Proteins are the most important organic compounds of the cell which carry out virtually all of the cell's activities. They constitute major part of the dry weight of a cell. Proteins are the complex organic compounds having C, H, O and Nas elements, sometimes they contains Salt, Despice large building blocks of tissues. Many parts of the body such as hair, nails and feathers are also protein. Whereas meat, fish, milk and pulses are the major source of protein. ### 1.4.1 Amino acid as a building block of protein Proteins are macromolecule or polymers of amino acids. These amino that proteins sequence of amino acids that gives the unique defined above peptide bond or peptide linkage. As we have properties to these molecules. There are twenty basic amino acids which