Biomolecules PDF

# Biomolecules Chemicals or molecules present in the living organisms are known as **Biomolecules**. - The sum total of different types of biomolecules, compounds and ions present in a cell is called as **cellular pool**. - Biomolecules are compounds of **carbon**. - Hence the chemistry of living...

# Biomolecules Chemicals or molecules present in the living organisms are known as **Biomolecules**. - The sum total of different types of biomolecules, compounds and ions present in a cell is called as **cellular pool**. - Biomolecules are compounds of **carbon**. - Hence the chemistry of living organisms is organized around carbon. - Carbon is the most versatile and the most predominant element of life. ## Elemental Composition of Earth Crust and Living Matter | Element | Non living (Earth crust) | Living Matter | |---|---|---| | Hydrogen | 0.14 | 0.5 | | Carbon | 0.03 | 18.5 | | Oxygen | 46.6 | 65.0 | | Nitrogen | Very less | 3.3 | | Sulphur | 0.03 | 0.3 | | Sodium | 2.8 | 0.2 | | Calcium | 3.6 | 1.5 | | Magnesium | 2.1 | 0.1 | | Silicon | 27.7 | Very less | ## Classification of Biomolecules - **Inorganic** - Minerals - Gases - Water - **Organic** - Carbohydrates - Lipids - Amino acids - Proteins - Enzymes - Nucleotides - Nucleic acids - Vitamins ## Biomolecules and their size - **Micro molecules** - Small sized, low mol wt - Between 18 and 800 daltons - Found in the acid soluble pool - Minerals - Gases - Water - Sugars - Amino acids - nucleotides - **Macromolecules** - Large sized, high mol wt - Above 10000 daltons - Found in the acid insoluble pool - Carbohydrates - Lipids - Proteins - Nucleic acids ## Major Complex Biomolecules of Cells | Biomolecule | Building block | Major functions | |---|---|---| | Protein | Amino acid | Basic structure and function of cell | | DNA | Deoxyribonucleotide | Hereditary information | | RNA | Ribonucleotide | Protein synthesis | | Polysaccharide | Monosaccharide | Storage form of energy | | Lipids | Fatty acids & glycerol | Storage form of energy to meet long term demands | ## Nucleotides A nucleotide comprises: - A **phosphate group** - A **sugar** - A **nitrogenous base** ### Sugar The sugar in nucleotides can be: - **Deoxyribose** - **Ribose** ### Nitrogenous Bases - **Purine (Parent Compound)** - Adenine (A) - Guanine (G) - **Pyrimidine (Parent Compound)** - Cytosine (C) - Uracil (U) (found in RNA) - Thymine (T) (found in DNA) ## Deoxyribonucleic acid (DNA) - A polymer of Deoxyribonucleotides. - Consists of two polynucleotide chains. - The chains are antiparallel. - They are coiled around each other, forming a double helix. - Each strand of DNA has a backbone of sugar and phosphate. - The Nitrogenous bases of the two strands are linked by Hydrogen bonds. - Adenine (A) pairs with Thymine (T) through two hydrogen bonds. - Guanine (G) pairs with Cytosine (C) through three hydrogen bonds. ## Ribonucleic acid (RNA) - A polymer of Ribonucleotides - Single stranded - Found in the cytoplasm and nucleus - There are three types of RNA: - **mRNA** (messenger RNA) - **tRNA** (transfer RNA) - **rRNA** (ribosomal RNA) ## Carbohydrates Carbohydrates are the most abundant organic molecules in nature. - The term carbohydrate is derived from the French term **hydrate de carbone** i.e. it is a hydrate of carbon or $C_n(H_2O)_n$. - Carbohydrates are defined as organic substances having C, H & O wherein H and O are in the ratio 2:1 as found in $H_2O$. ### Functions of Carbohydrates - Most abundant source of energy (4 cal/g) - Precursors for many organic compounds (fats, amino acids) - Present as glycoproteins and glycolipids in the cell membrane and functions such as cell growth and fertilization. - Present as structural components like cellulose in plants, exoskeleton of some insects, cell wall of microorganisms. - Storage form of energy (glycogen) to meet the energy demands of the body. ### Classification of Carbohydrates - **Monosaccharides**: Basic units of carbohydrates. Cannot be hydrolysed into smaller units. - Based on the number of C-atoms - Based on the type of functional group - **Oligosaccharides**: Can be further hydrolysed - Disaccharides - Trisachharides - Tetrasachharides - **Polysaccharides**: Non crystalline, non soluble in water, tasteless, on hydrolysis gives mol of monosaccharides e.g. starch, cellulose ### Polysaccharides - Also called as **Glycans**. - Made up of repeating units of monsaccharides held by glycosidic bonds. - During its formation a water molecule is released at each condensation. - This helps reduce the bulk making it almost insoluble decreasing its effect on the water potential or osmotic potential of the cell. - Unlike sugars they are not sweet. - They are ideal as **STORAGE AND AS STRUCTURAL COMPONENTS**. #### Types of Polysaccharides - **Homoglycans**: Made up of only 1 type of monosaccharide monomers. - For eg. starch, glycogen, cellulose. - Glucan (made up of glucose) - Fructan (made up of fructose) - Galactan (made up of galactose) - **Heteroglycans**: Made up condensation of 2 or more types of monosaccharides. - For eg. Hyaluronic acid, agar, Chitin, peptidoglycans etc ### Storage Polysaccharides - **Starch**: Carbohydrate reserve of plants and the most important dietary source for animals. - High content of starch in cereals, roots, tubers, vegetables etc. - Homopolymer made up of **GLUCOSE** units. Also called as **GLUCAN**. - Starch = Amylose + Amylopectin (polysaccharide components) - **Glycogen**: Carbohydrate reserve in animals. Hence referred as **animal starch**. - High concentration in Liver, muscles and brain. - Also found in plants that do not have chlorophyll (yeast and fungi). - **GLUCOSE** is the repeating unit. - **Inulin**: Polymer of fructose i.e. **fructosan**. - Found in Dahlia, bulbs, garlic, onion etc. - Easily soluble in water. - Inulin is not readily metabolised in the human body and is readily filtered through the kidney. Hence used for testing kidney function (GFR) ### Structural Polysaccharides - **Cellulose**: Occurs exclusively in plants and is the most abundant organic substance in plant kingdom. - Predominant constituent of plant cell wall. - It is totally absent in animals. - **Chitin**: Second most abundant organic substance. - Complex carbohydrate of Heteropolysaccharide type. - Found in the exoskeletons of some invertebrates like insects and crustaceans. Provides both strength and elasticity. - Becomes hard when impregnated with calcium carbonate. ## Proteins Proteins are the most abundant organic molecules of the living system. - They form about 50% of the dry weight of the cell. - They are most important for the architecture and functioning of the cell. ### Protein Structure and Function - Proteins are polymers of **amino acids.** - Proteins on complete hydrolysis yields **Amino Acids**. - There are 20 standard amino acids which are repeatedly found in the structure of proteins - animal, plant or microbial. - Collagen is the most abundant animal protein and Rubisco is the most abundant plant protein. - Protein Synthesis is controlled by DNA. ### Amino Acids Amino acids are a group of organic compounds having 2 functional groups (-NH2) and (-COOH). - (-NH2) group is basic whereas (-COOH) is acidic. - R- can be H in glycine, $CH3$ in alanine, Hydroxymethyl in serine. - In others it can be hydrocarbon chain or a cyclic group. - All amino acids contain C, H, O and N but some of them additionally contain S. - Physical and chemical properties of amino acids are due to amino, carboxyl and R functional groups. - Amino acids are differentiated into 7 groups. #### Classification of Amino Acids | No. | Nature | Amino acids | |---|---|---| | 1. | **NEUTRAL**: Amino acids with 1 amino and 1 carboxyl group | Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile) | | 2. | **ACIDIC**: 1 extra carboxyl group | Aspartic acid (Asp), Asparagine (Asn), Glutamic acid (Glu), Glutamine (Gln) | | 3. | **BASIC**: 1 extra amino group | Arginine (Arg), Lysine (Lys) | | 4. | **S – CONTAINING**: Amino acids have sulphur | Cysteine (Cys), Methionine (Met) | | 5. | **ALCOHOLIC**: Amino acids having -OH group | Serine (Ser), Threonine (Thr), Tyrosine (Tyr) | | 6. | **AROMATIC**: Amino acids having cyclic structure | Phenylalanine (Phe), Tryptophan (try) | | 7. | **HETEROCYCLIC**: amino acids having N in ring structure | Histidine (His), Proline (Pro) | ### Peptide Formation - Amino acids are linked serially by **peptide bonds** (-CONH-) formed between the (-NH2) of one amino acid and the (-COOH) of adjacent amino acid. - Chain having 2 amino acids linked by a peptide bond is called as a **DIPEPTIDE**. - The sequence of amino acids present in a polypeptide is specific for a particular protein. ### Structure of Protein 4 basic structural levels are assigned to proteins - primary, secondary, tertiary and quaternary: - **Primary structure**: Refers to the number and linear sequence of amino acids in the polypeptide chain and the location of the disulphide bridges. - **Secondary structure**: The folding of the linear chain into a specific coiled structure is called as secondary structure. - **α- helix**, **β- pleated sheet** and **collagen helix**. - **Tertiary structure**: The helical polypeptide may fold upon itself and assume a complex but specific form - spherical, rod like or something in between. These geometrical shapes are known as tertiary (3°) structure. - **Quaternary structure**: Proteins are said to be quaternary in structure if they have 2 or more polypeptide chains. Haemoglobin is an excellent example. ### Classification of Proteins - **Function**: - **Enzymatic proteins e.g. pepsin** - **Transport proteins e.g. Haemoglobin** - **Hormonal proteins e.g. Insulin, Growth hormone** - **Contractile proteins e.g. Actin, myosin** - **Storage proteins e.g. Ovalbumin** - **Genetic proteins e.g. Nucleoproteins** - **Defence proteins e.g. Imunoglobulins** - **Chemical nature and solubility**: - **Simple proteins**: They are composed only of amino acid residues. - **Globular**: - Albumin - Globulin - Histones - **Fibrous**: - Collagen - Elastin - Keratin - **Conjugated proteins**: Along with amino acids, there is a non-protein prosthetic group. - Nucleoproteins - Glycoproteins - Mucoproteins - Lipoproteins - Phosphoproteins - Chromoproteins - Metalloproteins - **Derived proteins**: They are denatured or degraded products of the above two. - **Primary**: - Coagulated proteins - Proteans - **Secondary**: - Proteoses - protones - Peptides ## Lipids Lipids are the chief concentrated storage form of energy forming about 3.5% of the cell content. - Lipids are organic substances relatively insoluble in water but soluble in organic solvents (alcohol, ether). ### Functions of Lipids - They are the concentrated **fuel reserve** of the body. - Lipids are **constituents of membrane structure** and regulate the **membrane permeability**. - They serve as source of **fat soluble vitamins**. - Lipids are important cellular **metabolic regulators**. - Lipids protect the internal organs and serve as **insulating materials**. ### Classification of Lipids - **Simple lipids**: They are esters of fatty acids with alcohol. - **Neutral or true fats**: Esters of fatty acids with glycerol. - **Waxes**: Esters of fatty acids with alcohol other than glycerol. - **Complex lipids**: They are derivatives of simple lipids having additional group like phosphate, N₂-base, Protein etc. - **Phospholipids** - **Glycolipids** - **Lipoproteins** - **Derived lipids**: They are derivatives obtained on the hydrolysis of the simple and complex lipids. - **Steroids** - **Terpenes** ### Simple Lipids #### True fats: - True fats are made up of C, H, & O but O is less. - A fat molecule is made up of 2 components: - **GLYCEROL**. - **FATTY ACIDS**: (1-3 mol, of same or diff long chained) ### Waxes - Lipids which are long chain saturated fatty acids and a long chain Saturated alcohol of high mol wt other than glycerol. #### Examples of Waxes - Bees wax: secretion of abdominal glands of worker honey bees. - Lanolin or wool fat: Secretion of cutaneous glands and obtained from the wool of sheep. - Sebum: secretion of sebaceous glands of skin. - Cerumen: soft and brownish waxy secretion of the glands in the external auditory canal. Also called as Earwax. - Plant wax: Coating formed on the plant organs to prevent transpiration. - Paraffin wax: A translucent waxy substance obtained from petroleum. ### Complex Lipids - They are derivatives of simple lipids having additional group like phosphate, N₂-base, Protein etc. - They are further divided into Phospholipids, Glycolipids, Lipoproteins. #### Phospholipids - They are made up of a molecule of glycerol or other alcohol having: - A phos group at 1 of its -OH groups. - 2 fatty acid molecules at other 2 -OH groups. - A nitrogen containing base attatched to phos group. - A phospholipid molecule has a **hydrophobic tail** (fatty acids) and a **hydrophilic head** (phos group). #### Glycolipids - Components of **cell membranes**, particularly myelin sheath and chloroplast membranes. - **CEREBROSIDE** are the most simplest form of glycolipids. #### Lipoproteins - They contain lipids and proteins in their molecules. - They are main constituent of membranes. - They are found in milk and Egg yolk. - Lipids are transported in blood and lymph as lipoproteins. ##### Types of Lipoproteins: - chylomicrons - VLDL - LDL - HDL - Free fatty acid albumin complex ### Derived Lipids - They are derivatives obtained on the hydrolysis of the simple and complex lipids. - e.g. steroids, terpenes and **prostaglandins**. #### Steroids - The steroids do not contain fatty acids but are included in lipids as they have fat-like properties. - They are made up of **4 fused carbon rings**. - Cholesterol, Vit D, testosterone, adrenocortical hormones. - The most common steroids are **STEROLS**. - Common sterols are **Cholesterol** and **ergosterol**. #### Terpenes - Terpenes are a major component of essential oils produced by plants. They give fragrance to the plant parts. - Vitamins A, E and K contain a terpenoid called **phytol**. - **Carotenoid** pigment is precursor for Vitamin A. - **Lycopene**, a pigment present in tomatoes is a terpenoid. - **Gibberellins**, the plant hormone is also a terpene. ## Enzymes Enzymes are a group of catalysts functioning in a biological system. - They are usually proteinaceous substances produced by the living cell without themselves getting affected. - Enzymes enhance the rate of reaction and are formed in the cell under the instructions of genes. - **ENZYMOLOGY** is the branch of science that deals with the study of Enzymes in all the aspects like nomenclature, reactions and functions. - Enzymes occur in colloidal state and are often produced in inactive form called **proenzymes** (**zymogen**), which are converted to their active forms by specific factors like pH, substrate etc. - The enzymes that are produced **within** a cell for metabolic activities are known as **endoenzymes** and those which act **away** from the site of synthesis are called **exo-enzymes**. ### General Properties of Enzyme and Factors Affecting Their Activity 1. **Enzymes accelerate** the reaction but do not initiate it. 2. Enzymes themselves do not participate in the reaction and remain **unchanged** at the end of the reaction. Enzymes, are therefore, needed in **small amounts**. 3. The molecule of an enzyme is **larger** than that of substrate molecule and hence during reaction a specific **part** of enzyme molecule comes in contact with the substrate molecule. That part is called **active site** of enzyme. 4. **Amphoteric nature**: Chemically most of the enzymes are proteins and, therefore, show amphoteric nature. The enzymes can react with **acidic substances** as well as **alkaline substances**. 5. **Specificity**: Most of the enzymes are specific in their action. A single enzyme acts upon a **single substrate** or a group of closely related substrates. - For example, the enzyme urease can act only upon urea. - invertase can act upon sucrose only - A slight change in the configuration of the substrate molecule requires action by a different enzyme. 6. **Colloidal nature**: All enzymes are colloidal in nature and thus provide **large surface area** for reaction to take place. Colloids (colloids- gel like) are mixtures of two components i.e. dispersed particles and dispersion medium. The size of the dispersed particles is **larger** than dispersion medium. 7. **Enzyme optima**: Enzymes generally work best under certain **narrowly defined conditions** referred to as optima. These include appropriate temperature and PH. - **Temperature sensitivity**: Since the enzymes are proteins, they are affected by change in temperature. With increase in temperature, **increase** in enzyme activity takes place (up to 40 C). However, when temperature increases **above 60 C** the proteins undergo **denaturation** or even complete **breakdown**. When the temperature is reduced to freezing point or below freezing point the enzymes become **inactivated** but they are not destroyed. The rate of reaction is more at optimum temperature. - **pH sensitivity**: Most of the enzymes are specific to pH and remain active within particular range of pH. The strong acid or strong base denatures enzymes. Most of the intracellular enzymes function best around **neutral pH**. 8. **Concentration of enzyme and substrate**: The rate of reaction is proportionate to the concentration of the reacting molecules. If the **substrate concentration** is increased the rate of **enzyme action** also increases up to certain limit. Beyond a certain concentration, the enzyme molecules remain saturated with substrate molecules and the activity becomes steady. 9. **Enzyme inhibitors**: Enzyme inhibitors are certain products which inhibit enzyme activity. During the reaction, if the **active site** of enzyme is occupied by these **inhibitors** instead of substrate molecules and the **activity** of enzyme is lost. These substances are like substrate molecules in their **structure** and are called **competitive inhibitors**. ### Classification of Enzymes - **Oxidoreductases**: Transfer of O2 or H2 atoms or electrons from one substrate to another. - Dehydrogenase - Oxidases - **Transferases**: Transfer of a specific group from one substrate to another. - Transaminase - **Hydrolases**: Hydrolysis of a substrate. - Digestive enzymes - **Isomerases**: Change of the molecular form of the substrate. - Phospho Hexo isomerase - **Lyases**: Non hydrolytic removal or addition of a group to a substrate. - Decarboxylase - Aldolase ## Mechanism of Enzyme Action - Enzymes can lower the activation energy of a reaction - Enzymes bind to their substrates at the **active site**. - An **enzyme-substrate complex** is formed. - The bonds in the substrate are weakened. - This leads to the formation of **products**. - The enzyme is then released and can catalyze another reaction.