BIOLOGY CLASS NOTES FOR CBSE Chapter 09. Biomolecules 01. Carbohydrates These are the compound of carbon, hydrogen and oxygen having hydrogen and oxygen in the same ratio as that of water, i.e. 2 : 1. They are among the most widely distributed compound both in plant as well as animal kingdom. On the basic of their reducing properties carbohydrates can be of two types, i.e. reducing sugar and non-reducing sugar. Carbohydrates
Non-reducing sugar
Reducing sugar Ÿ Ÿ Ÿ
These are the sugars with free aldehyde (−CHO) or keto groups > C=0 They can reduce (Cu2+) to cuprous Cu+ ion. They reduce Fehling's solution and Benedict reagent. e.g. all monosaccharides,
Ÿ Ÿ Ÿ
These sugar do not have free aldehyde or keto group. They cannot reduce the Fehling solution and Benedict reagent. e.g. sucrose. They do not reduce the Fehling solution and Benedict reagent. e.g. sucrose.
On the basis of hydrolysis, products of carbohydrates, products of carbohydrates can be monosaccharides, oligosaccharides and polysaccharides
Monosaccharides These are simple carbohydrates that cannot be hydrolysed further into smaller units. They consists of a single polyhydroxy aldehyde or ketone unit. These are mostly made up of 3-7 carbon atoms. (i) Based on the number of carbon atom the monosaccharides are regarded as (a) Trioses having 3C atoms, e.g. glyceraldehyde and dihydroxyacetone. (b) Tetroses having 4C atoms, e.g. thriose and erythrose (c) Pentose having 5C atoms, e.g. ribose, ribulose (d) Hexoses having 6C atoms, e.g. glucose, galactose and mannose
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CLASS NOTES FOR CBSE – 09. Biomolecules
(i)
Pyranose ring which has hexagonal shape with 5C and 1 oxygen atoms.
(ii)
Furanose ring which has pentagonal shape with 4C atom and 1 oxygen atom.
Oligosaccharide These are formed by the condensation of 2-9 monosaccharide units. In oligosaccharides these units are held together by glycosidic bonds. (i) Disaccharide, e.g. sucrose, maltose, lactose, trehalose, etc. (ii) Trisaccharide, e.g. raffinose. (iii) Tetrasaccharide,, e.g. stachyose.
Polysaccharide or Glycans These are polymers or chains of monosaccharides (usually more than9) bound in linear or branched chain pattern. Homoglycans or Homopolysaccharide They are the polysaccharide, which are formed by the polymerisation of only one type of monosaccharide unit, e.g. starch, glycogen, cellulose, callose, etc. (i) Starch It is a polymer of D-glucopyranose units liked by 4- glycosidic linkages. It consists of a mixture of amylose and amylopectin in 1 : 4 ratio. Amylose is linear and consists of about 200-500 glucose unit, on the other hand amylopectin is branched and consists of over 1000 glucose units.
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(ii)
(iii) Glycogen It found mainly in mainly in liver and muscles. About 5000-15000 glucose units make up a glycogen molecule. It is a non-reducing sugar that gives red colour with iodine. (iv) Cellulose It is the most important structural component of the cell wall o plants. It is a linear polymer of glucose unit connected through 4- glycosidic linkages.
Heteroglycans or Heteropolysaccharide They are the complex polysaccharide, Which are formed by the polymerisation of two or more types of monosaccharide unit,
02. Amino Acids These are small molecule made up of carbon, hydrogen, nitrogen, oxygen and in some cases sulphur also. They are considered to be the first molecule formed in the atmosphere of the earth. They serve as monomers of proteins.
Structure Amino acids are also referred as substituted methane. Each amino acid has a free carboxyl group, a free amino group and ‘R’ as the distinctive side chain (variable). All these components are attached to a central carbon atom called α-carbon atom. Based on the nature of R group, a variety of amino acids are classified. The R in the amino acid could be a hydrogen or aliphatic, aromatic or heterocyclic group. The amino group imparts a basic character to amino acid. On the other hand carboxylic group gives it acidic character.
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CLASS NOTES FOR CBSE – 09. Biomolecules
Classification of amino acids On the basis of their synthesis in the body of living organism On the basis of synthesis in living organism, amino acids are classified into following three categories. (i) Essential amino acids can be synthesised by any organism in the body and are to be obtained from dietary sources. They are 8 in case of animals and 7 in case of humans. (ii) Non-essential amino acid can be synthesised by an organism and thus, is not required as dietary component. They are 10 in numbers. (iii) Semi-essential amino acid required essentially by an organism during particular phase of body growth and lactation period (in pregnant mothers). They are 2 in numbers. On the basis of chemical nature On the basis of chemical nature amino acids are as follows (i) Neutral : They have one amino group and one carboxyl group (monoamino monocarboxylic) with non-cyclic hydrocarbon chain, e.g. glycine (simple amino acid), alanine, valine leucine and isoleucine. (ii) Acidic : They have an additional carboxylic group (monoamino dicarboxylic), e.g. aspartic acid, glutamic acid, aspargine and glutamine. (iii) Basic : They have additional amino group without forming amides (diamino monocarboxylic), e.g. arginine and lysine. On the basis of side chain On the basis of side chain, amino acids are of following types (i) Sulphur containing : They possess sulphur, e.g. cysteine and methionine. (ii) Alcoholic : They possess alcohol or hydroxyl group, e.g. threonine, tyrosine and serine. (iii) Aromatic : They possess a cyclic structure (or group) inside chain, e.g. phenylalanine, tryptophan and tyrosine. (iv) Heterocyclic : They possess a cyclic ring (or group) bearing nitrogen, e.g. histidine, proline and tryptophan. Zwitter ion and isoelectric point Amino acids can act as both acids and bases as they contain one amino and one carboxylic group. Thus, they behave differently in solutions of different pH. In a neutral solution the amino acid molecule exists as a dipolar ion (Zwitter ion), i.e. a molecule containing positive and negative ionic group. R
R
R
HN3+―CH―COOH ⇌ H3+N―CH―COO− ⇌ HN―CH―COO− Cation (low pH)
Zwitter ion (at isoelectronic pH)
Anion (high pH)
03. Proteins The term ‘protein’ was first coined by Berzelius (1837) and Mulder (1838). Proteins are involved in structural support, storage, transport, signalling, movement, etc. in living organisms.
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Peptide bond A peptide bond (C―N) is formed between the nitrogen atom of amino group of one amino acid and the carbon atom of carboxylic group of another amino acids as shown below
Structural levels in protein (i)
(ii)
Primary structure The primary structure of a protein is its linear chain amino acids. The first (extreme left) amino acid of the chain is known as N-terminal amino acid with its unbonded amino group. Likewise the last one (extreme right) as C-terminal amino acid with its unbonded COOH group. Secondary structure The longer polypeptide chains are usually folded or coiled to produce specific structures referred as secondary structures. Three major types of secondary structure α-helix, β-pleated sheet and tropocollagen helix have been identified. (a) α-Helix : In this, the chain is coiled spirally, generally in the right-handed manner. At places, the helix is less regular forming random coils. This structure is formed through H-bonding in single amino acid chain only. This kind of secondary structure is found in several proteins, such as keratin (entirely helical), myosin, topomyosin, fibrin, epidermis, etc. (b) β-Pleated sheets : When two or more polypeptide chains are held together by intermolecular H-bonds the structure is called as β-pleated sheet. They can be classified as β-pleated sheets
β-parallel sheets adjacent strand of polypeptide runs in the same direction, e.g. β-keratin. These are less stable.
β-antiparallel sheets Adjacent strand of polypeptide runs in the opposite direction, e.g. fibroin of silk. These are more stable.
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(c) Collagen or Tropocollagen helix : It is a special secondary structure observed in the collagen having three strand or polypeptide chains coiled around one another. The coil is strengthened by the establishment of H-bonding mainly between hydroxyproline and proline residues. (iii) Tertiary structure The polypeptide chain may undergo further coiling and folding to produce the 3-dimensional structure of protein. The tertiary structure determines the overall shape of a protein molecule. Proteins are called fibrous proteins, when they form thin, long threads and globular proteins, if they are compact. These structures are stabilised by several types of bonds namely hydrogen bond, ionic bond, vander Waal’s interaction, covalent bond and hydrophobic bond. (iv) Quaternary structure Protein is said to be in quaternary structure, if it consists of two or more polypeptide chains united by the forces other than covalent bond, (i.e. neither peptide nor disulphide).
04. Lipids These are heterogenous group of compound having one characteristic in common, i.e. their hydrophobic nature. They are made up of carbon, hydrogen and oxygen. The count of oxygen in them is always less as compared to the number of carbon atom. These are insoluble in water, but are readily soluble in non-polar organic solvent such as chloroform, benzene and ether.
Fatty acids These are water insoluble long chain hydrocarbons (4-36 carbon long) with one carboxyl (―COOH) group. These are the simplest constituents of lipids. Fatty acid chains may be of following two types.
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Classification of Lipids (i)
(ii)
Simple lipids : They are the esters of fatty acids with alcohol. These are of two types: (a) Fats, are esters of higher fatty acid with glycerol, i.e. triglycerides (b) Waxes, are esters of higher fatty acids with alcohol other than glycerol in them. Compound or conjugated lipids : These are esters of fatty acids with alcohol, but contain some other substances also. They are of following types. (a) Phospholipids : These are made up of a molecule of glycerol or other alcohol. This lipid essentially consists of Ÿ a phosphate group joined to one of its outer―OH group. Ÿ two fatty acid molecules linked to each other with two―OH groups. Ÿ a nitrogen containing base such as choline molecule, bound to the phosphate group. Phospholipids are found in cell membranes, e.g. lecithin. (b) Glycolipids : These contain fatty acids, alcohol sphingosine and a sugar (galactose). The sugar replaces one fatty acid molecule. These lipids are present in myelin sheath of nerve fibres, and on the outer surface of cell membrane of chloroplast. (c) Lipoproteins : These contain lipids (mainly phospholipids) and proteins in their molecules. Most membranes are composed of lipoprotein. (d) Chromolipids : These contain pigments such as carotenoids, e.g. carotene, vitamin−A. (a) (b) Prostaglandins : These are biologically active lipids first discovered in human seminal fluid. All mammalian cells except RBC produce prostaglandins. These are involved in binding of hormones to the membranes. They are derived from arachidonic acid (C20 fatty acid). (c) Terpenes : These are essential oil and mostly present in oils of camphor, mint, lemon and eucalyptus. Phytol a terpenoid is present in vitamin A, E and K.
05. Nucleic Acids They constitute the genetic material of all living organism. The two most important nucleic acid present in living cell are deoxyribonucleic acids (DNA) and ribonucleic acid (RNA). DNA and RNA were discovered by Friedrich Miescher in 1969. A nucleotide is composed of following three molecules. (i) Phosphoric acid, i.e. H3PO4 with 3 reactive −OH groups. Out of these 2 are involved in forming sugar phosphate backbone with the help of phosphodiester linkages (―C―O―P―O―C―).
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(ii)
Pentose sugar, i.e. the carbohydrate (monosaccharide) with 5 C atoms. This may be deoxyribose in DNA or ribose in RNA. Both of these sugars differ as shown.
(iii) Nitrogenous bases, i.e. the heterocyclic organic bases, that contain nitrogen in them. There are five different bases, which are categoriesed into two types, i.e. purines and pyrimidines. (a) Purines are double-ring bases. The two purines are adenine and guanine.
(b) Pyrimidines are single ring bases, which include cytosine, thymine and uracil of these nitrogenous bases, DNA consists of adenine, guanine, cytosine and thymine, whereas RNA contains adenine, guanine, cytosine and uracil. Nucleoside + Phosphate group = Nucleotide.
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DNA It is the main genetic material of living beings. In prokaryotes it is present without any association with proteins. Structure The most widely accepted structural model of DNA is the double-stranded double helical model of Watson, Crick and Wilkins (1953). According to the model proposed by Watson and Crick (i) The DNA molecule consists of two helically twisted antiparallel strands connected together via base pairs. (ii) The twisting or coiling of strands results into formation of deep (major) and shallow (minor) grooves as shown in the figure below
(iii) Each strand of DNA consists of alternating molecules of deoxyribose sugar and phosphate groups. The linkage between the sugar and phosphate molecule is called phosphodiester linkage. In this linkage the phosphate group is attached to 3rd C-atom of one sugar molecule and 5th C-atom of other molecule as shown below (iv) The two strands are interwined in a clockwise direction, i.e. in the form of a right-handed helix and have antiparallel arrangement. This right-handed form of DNA is called as B-DNA and left-handed form is called A-DNA. (v) DNA has a uniform thickness of 2nm (20Å). Its pitch or 1 turn is about 0.34 nm. Thus, 2 successive bases in DNA are 3.4 nm apart as each turn consists of 10 nucleotides.
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Bonds in DNA structure The bonds seen in DNA structure are as follows (i) Hydrogen bonds (a) 3 Between G and C at 1st, 2nd and 6th position (b) 2 Between A and T at 1st and 2nd position (ii) True covalent bonds (a) Between Sugar – Purine at 1:9 position. (b) Between Sugar – Pyrimidine 1:3 position. (c) Sugar – Phosphate – Sugar i.e., phosphodiester linkage → 3-5 linkage.
RNA The other nucleic acid present in the cell is RNA, i.e. ribose nucleic acid. The RNA can be of following three types (i) Messenger RNA or mRNA or template RNA (ii) Ribosomal RNA or rRNA (iii) Soluble-RNA or transfer-RNA (s or tRNA) The three types of RNA are synthesised during different stages of embryonic development. The mRNA is synthesised during cleavage, tRNA is synthesised at the end or cleavage, while rRNA is synthesised during gastrulation. Messenger RNA or mRNA The name messenger RNA was proposed by Jacob and Monod in 1961. It makes 3-5% of total cellular RNA. The sedimentation coefficient of mRNA is 8 S. It is always single-stranded, and without any base pairing, because base pairing in mRNA stand can destroy its biological activity. The structural components or mRNA include (i) A cap is present at th 5′ end. It controls the rate of protein synthesis. Without the cap, mRNA molecules bind very poorly to ribosomes. The cap is rich in methyl residues. (ii) Cap is followed by non-coding region of 10 to 100 nucleotides. This region is rich in A and U residues. It does not have ability to translate protein. (iii) The non-coding region terminates at initiation codon AUG (sometimes GUG or UUG also) in both prokaryotes and eukaryotes. (iv) With the initiation codon, the coding region begins, which contains on an average about 2500 nucleotides. The coding region terminates at termination codon, i.e. either of UAA, UAG, UGA. (v) The length of mRNA decreases with age. mRNA can be of two types (a) Monocistronic, i.e. single molecule formed by one gene as in eukaryotes. (b) Polycistronic, i.e. single molecule formed by many genes as in prokaryotes. (vi) The mRNA of prokaryotes is considered to be metabolically unstable. It does not stay for long in the body or prokaryote and gets destroyed readily even during the continuation of metabolic process itself. On the other hand, the mRNA of eukaryotes is considered as metabolically stable, as it normally waits for the completion of process concerned.
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Ribosomal RNA or rRNA The rRNA makes 80% or more of total cellular RNA. This is the basic constituent of ribosomes and developes from the Nucleolar organiser region of chromosomes in eukaryotes. In prokaryotes, it is developed from rDNA. This RNA is seen as a compact rod or coil or in the form of extended regions. The structure actually depends upon various factors like ionic strength, pH, temperature, etc. Soluble RNA or sRNA It makes about 10-20% of total cellular RNA with sedimentation coefficient of 3.8 S. A tRNA molecule has following four recognition sites namely (i) Amino acid binding site (CGA) (ii) Ribosome recognition site (GT ψ CR) (iii) Anticodon site (iv) Synthetase site This RNA contains 73-93 nucleotides within the structure. The tRNAs, which carry amino acids for initiation codon are called initiator tRNA. The function of tRNA is to align the required amino acid according to nucleotide sequence of mRNA. During this aligment, the ribosome is also present. tRNA is also the carrier of the activating enzyme of amino acid.
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CBSE Pattern Exercise (1) (Q 1 to 3) One Mark 1. What is an apo-enzyme? 2. What is ligase? 3. Monosaccharides are called ‘reducing sugars’ but disaccharides are not. Why? Write an example of each type of sugar. (Q 4 to 6) Two Marks 4. What are the two advantages of storing carbohydrates in the form of polysaccharides? 5. What is the name given to the part of enzyme where catalystic work is carried out? 6. How do Animals digest cellulose? (Q 7 to 8) Three Marks 7. What is contact catalysis? 8. Write the differences between enzymes and catalysts. (Q 9 to 10) Five Marks 9. In the stomach and small intestine, the enzymes for digestion of proteins are secreted in an inactive form. Why? 10. Why doesn’t oil dissolve in water. Give a scientific explanation.
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ANSWER Q1 A protein that combines with a coenzyme to form an active enzyme is called apo-enzyme. Q2 An enzyme that can rejoin a broken phosphodiester bond in a nucleic acid is called ligase. Q3 Monosaccharides are called reducing sugars because they have a free aldehyde or ketone group and can reduce Cu++ to Cu+. Example: Glucose. But disaacharides like sucrose do not reduce Cu++ to Cu+. Hence, it is not a reducing sugar. Q4 The two advantage of storing carbohydrates in the form of polysaccharides are, (i) The polysaccharides are starch and glycogen. Starch is found in rice, wheat, etc. Glycogen is stored in liver. During the formation of molecules, the water is removed from the monosaccharides. (ii) If necessary, polysaccharides are broken down by enzymes for release of energy. Q5 Active site is that part of enzyme where catalytic work is carried out. An enzyme may have one or more active sites. The active site of aldolase contains glycine. histidine and alanine a group of three amino acids. Q6 A number of mammals- ruminants such as cows and other herbivorous animals are capable of digesting the cellulose with the help of microorganisms present in their digestive tract. Snail and termites also digest cellulose with the help of microorganisms present in them in the digestive tract. Q7 In biochemical reactions, the enzyme absorbs the reactant or substrate molecules over its active sites so as to bring them closer for chemical reaction. This phenomenon is called contact catalysis. Q8 Enzymes Catalysts All enzymes are made up of proteins Catalysts are inorganic and small having complex structure. moleculse having simple structure. Ezymees are specific in their action. They catalyse many reactions. Q9 In the stomach and intestine, the enzymes, which act on proteins are pepsin and trypsin. These are secreted in the inactive form. The inactive form of pepsin is pepsinogen and the inactive form of trypsin is trypsinogen. These require the help of certain activators to become active. For example, when food reaches the stomach, another set of glands secrete HCl in small quantities. HCl activates
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the pepsinogen and converts it into pepsin. It can act only in an acidic medium on proteins in order to digest them. Similary, trypsin secreted by the pancereas in an inactive form is known as trypsinogen. When it comes in contact with another enzyme, enterokinase secreted by the mucosal layer of the duodenum, it gets converted into active trypsin. In the intestine, trypsin can act only in the alkaline medium. Q10 Water molecules are interconnected with hydrogen bonds giving a lattice structure. Its fluidity is maintained by rapid formation by rapid formation and dissociation of hydrogen bonds between the water molecules. Now in order to dissolve a substance in water, it water, it should be able to form a new hydrogen bond with a water molecule so as t become a part of its lattice. But this is possible only for hydrophilic groups. Oils being hydrophilic and-polar compound, they are unable to join with the lattice structure of water. Hence, it doesn’t dissolve but floats on water.
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