Biomolecules (PDF)

# BIOMOLECULES ## **Ch-9 BIOMOLECULES** - The carbon compounds that we get from living tissues can be called Biomolecules. - Biomolecules can be divided into 2 categories: - **Inorganic Biomolecules** Include water, minerals, CO₂ etc. - **Organic Biomolecules** Includes Carbohydrat...

# BIOMOLECULES ## **Ch-9 BIOMOLECULES** - The carbon compounds that we get from living tissues can be called Biomolecules. - Biomolecules can be divided into 2 categories: - **Inorganic Biomolecules** Include water, minerals, CO₂ etc. - **Organic Biomolecules** Includes Carbohydrates, Lipids, Nucleic acids etc. ## **HOW TO ANALYSE CHEMICAL COMPOSITION OF A LIVING TISSUE?** - To do the chemical analyses, first take the living tissue and grind it with a mortar and pestle. - Then use a cheese cloth or cotton to filter the obtained slurry. ### **Obtained 2 Fractions:** 1. **Filtrate or Acid soluble Pool:** It contains molecules having low molecular weight (18 - 800 Dalton). 2. **Residue or Acid Insoluble Pool:** It contains macromolecules such as proteins, nucleic acid, polysaccharides, lipids etc. ## **TYPES OF BIOMOLECULES BASED ON MOLECULAR WEIGHT:** - **Micromolecules:** - They have low molecular weight, less than 1000 Dalton. - They are found in acid soluble fraction. Examples: amino acids, nucleotides, fatty acids, monosaccharides. - **Macromolecules:** - They have molecular weight above 800 Dalton - They are found in acid insoluble fraction. Examples: carbohydrates, proteins, nucleic acids and lipids. ***NOTE:*** Dipids have molecular weight less than 800 Dalton yet they are placed among the macromolecules due to their insoluble nature. ## **METABOLITES** - Biomolecules which are indued or catalysed in the metabolic reaction of the body are called metabolites. - They can be divided into two types: ### **1) Primary Metabolites:** - Molecules having identifiable functions and play specific roles in normal physiological processes - Examples: Amino acids, proteins, nucleic acids ### **2) Secondary Metabolites:** - They are not directly involved in growth and development. - They have no identifiable function. - Examples: Rubber, gums, antibiotics, pigments etc. #### **Prepare a table of secondary metabolites along with their examples:** | Polymeric Substance | Examples | |---|---| | Pigments | Carotenoids, Anthocyanins, etc. | | Alkaloids | Morphine, Codeine, etc. | | Terpenoides | Monoterpenes, Diterpenes, etc. | | Essential oils | Lemon grass oil, etc. | | Toxin | Abrin, Ricin, etc.| | Lectins | Concanavalin A, etc. | | Drugs | Vinblastin, curcumin, etc. | | Rubber gum, cellulose | | ## **EXPERIMENT TO PROVE THAT LIVING CELLS HAVE INORGANIC ELEMENTS:** - Take a small amount of living tissue (leaf). - Weigh it: fresh weight or wet weight - Dry it to get dry weight - Burn the tissues so that all the water vaporates - Oxidise to CO₂ and water. - The remaining matter is called "ash" which contains inorganic components. This ash contains inorganic components like Magnesium (Mg). ## **AMINO ACID** - Organic compounds containing a amino group (NH₂) and a carboxyl group (COOH) as substituents on the same carbon atom. (i.e. substituted methane) - Chemically they are substituted methane in all the four atoms in methane are substituted by H, a carbonyl group, an amino group and an R group (any group). - Based on the nature of R group, Amino acids are of 20 types - Based on the number of amino and carbonyl group, amino acids can further be divided into 3 types: 1. **Neutral amino acid** (Eg: Valine) 2. **Acidic amino acid** (Eg: Glutamic acid) 3. **Basic amino acid** (Eg: Lysine) ## **TYPES OF AMINO ACIDS BASED ON WHERE IT IS SYNTHESIZED:** ### **1) Essential Amino Acids:** - These are amino acids that cannot be synthesized in our body. - They have to be taken in the form of diet. - They are 10 in no. ### **2) Non-Essential Amino Acids:** - These amino acids can be synthesized by the body of a living organism. - They need not to be taken from outside. #### **NOTE:** - The 10 essential amino acids are: Phenylalanine, Valine, Tryptophane, Methionine, Leucine, Lysine, Isoleucine, Threonine, Histidine and Arginine. ## **PROPERTIES OF AMINO ACIDS** 1. **Amino acids show amphoteric properties:** - It can act as an acid as well as base and can forms zwitter ions. - It can exist in zwitter ion forms i.e. having both -ve charge and +ve charge group. ## **PROTEINS:** - Proteins are polymers of monomer called amino acids linked together by Peptide bond. - They are also called polypeptide. - Proteins are heteropolymers of different amines acids. <br> ## TYPES OF PROTEINS/LEVEL OF PROTEIN STRUCTURE: ### **1) Primary Structure:** - In this structure/line of protein, the amino acids are arranged in linear order with no folding. - It gives protein positional information of amino acid in which amino acid is the first, which is second and so on. ### **2) Secondary Structure:** - Protein structure formed by folding of polypeptide thread either into helix or into beta pleated sheets. - They are called secondary structure. ### **3) Tertiary Structure (3⁰):** - It is the structure of proteins formed by further folding of secondary structure. - Tertiary structure is stabilized by several types of bonds like hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interaction. - Only after attaining this structure, a protein becomes biologically active and functions for the students. ### **4) Quaternary Structure:** - Different proteins in their tertiary structure interact to form the quaternary structure. - Examples: Hemoglobin (Hb) is the quaternary structure of 4 polypeptide chains (2 alpha chain & 2 beta chain). - It is the most stable structure of proteins ## **CARBOHYDRATES (Saccharides)** - Carbohydrates are organic compounds made up of carbon, hydrogen, and oxygen where they are in the ration 1:2:1. - They are poly hydroxy aldehydes or ketones. - Carbohydrates are hydrates of carbons. ## **TYPES OF CARBOHYDRATES:** - Carbohydrates can be divided into 3 categories based on how much molecules they give on hydrolysis: 1. **Monosaccharides:** - They cannot be hydrolysed further. - They are made up of single unit. - Examples: glucose & fructose 2. **Oligosaccharides:** - These are sugars formed by linking 2-8 monosaccharide units. - The individual units are linked together by **Glycosidic bond**. - Examples: Sucrose, Maltose, Lactose, etc. 3. **Polysaccharides:** - They are complex sugars formed by linking many monosaccharides. - Examples: starch, cellulose, glycogen, etc. ## **MONOSACCHARIDES:** - They are carbohydrates made up of single unit. - They have general formula C_nH_2nO_n where (n = 3-7). - When n = 3, the carbohydrate is C₃H₆O₃ - we called it **Trioses**. - Example: Glyceraldehyde. - When n = 4, the carbohydrate is C₄H₈O₄ - we called it **Tetroses**. - Example: Erythrose. - When n = 5, the carbohydrate is C₅H₁₀O₅ - we called it **Pentose**. - Example: Ribose and deoxyribose. - When n=6, the carbohydrate is C₆H₁₂O₆ - we called it **Hexoses**. - Example: Glucose, Fructose etc. - When n = 7, the carbohydrate is C₇H₁₄O₇ - we called it **Heptoses**. - Example: Heptaglucose. ## **GLUCOSE:** - It is also called blood or grape sugar. - They are hexoses which can either be straight chain or ring form. - Depending upon the position of OH group at C-4 glucose can be of two types: - 1) **α-Glucose** (on below the plane) - 2) **β-Glucose** (on above the plane) ## **FRUCTOSE:** - It is also a hexose sugar (C₆H₁₂O₆). - It is one of the sweetest naturally occurring sugars. - It has got a ketone group instead of aldehyde group. - They are also reducing sugar. ## **OLIGOSACCHARIDES:** - They are carbohydrates form by linking 2-8 monosaccharides by Glycosidic bond. ### **NOTE:** - Glycosidic bonds are the bonds form by the condensation of monosaccharides units. - The bonds that form between 2 monosaccharides units are called Glyco-side bonds. - Oligosaccharides can be further divided according to the number of monosaccharide monomers. ### **DISACCHARIDES:** - These are disaccharides made up of 2 monosaccharides. #### ** Examples: Sucrose, Maltose, Lactose etc.** #### **Maltose = Glucose + Glucose** - The reaction: <br> > HO-CH2 > | > H-C--OH > | > HO-C-H > | > H-C-OH > | > CH₂OH > | > + > HO-CH₂ > | > H-C--OH > | > HO-C-H > | > H-C-OH > | > CH₂OH > | > → > HO-CH₂ > | > H-C--OH > | > HO-C-H > | > H-C-OH > | > CH₂OH > | > + H₂O > | > HO-CH2 > | > H-C--OH > | > HO-C-H > | > H-C-OH > | > CH₂OH > | - **Sucrose = Glucose + Fructose** - **Lactose = Glucose + Galactose** #### **Inulin = Fructose + Fructose** - It is a β (1 → 4) glycosidic bond. ## **POLYSACCHARIDES:** - They are complex sugars formed by linking many monosaccharides - Each monosaccharide unit is termed as monomer - individual unit. - They are formed by linking many monosaccharides units through complex glycosidic bonds. ### **1) Homopolysaccharide/Homopolymers:** - Only one type of monosaccharide is used to form the polysaccharide. - Example: starch, glycogen, inulin, etc. ### **2) Heteropolysaccharide:** - They are made up of more than one type of monosaccharides. - Example: Cellulose, Chitin, Pectin, Peptidoglycan, etc. ### **Starch:** - Made up of 200-200000 α-Glucose units. - It can either form straight chain (Amylose) or branch out (Amylopectin). - Connected by α (1→4) and α(1→6) Glycosidic bond. - Slightly digestible. ### **Cellulose:** - Made up of 6000 β-Glucose units. - It can only form straight chain - Connected by β (1→ 4) Glycosidic bond. - Difficult to digest. ### **Glycogen:** - Reserve foods of animal cells - Much branched ### **Starch Vs Glycogen:** - Main reserve food of plant - Amylose unbranched, Amylopectin less branched ## **NUCLEIC ACIDS:** - Nucleic acids are polymers of nucleotides linked together by phosphodiester bond. - A nucleotide is made up of 3 components: 1. **Pentose Sugar:** - Ribose - Deoxyribose 2. **Nitrogenous base:** - **Purine (A & G):** - Adenine - Guanine - **Pyrimidine ( T, U & C):** - Thymine - Uracil - Cytosine 3. **PO₄^3-:** -**Nucleotide** = Pentose Sugar + N-base + PO₄^3- -**Nucleoside** = Sugar + N-base - It is a nucleotide without PO₄^3- ## **STRUCTURE OF NUCLEIC ACIDS** <br> ## **TYPES OF NUCLEIC ACIDS:** - **DNA (Deoxyribonucleic Acid):** - It is double stranded (i.e. it has 2 nucleic acid chains) - The sugar is deoxyribose - The nitrogenous bases are adenine, guanine, cytosine and thymine. - Purine and pyrimidine are always in equal proportion. - It acts as genetic materials in all living organisms. - **RNA (Ribonucleic Acid):** - It is single-stranded. - The sugar is ribose. - The nitrogenous bases are adenine, guanine, cytosine, and uracil. - Do not maintain equal proportion. - It acts as genetic material only in some viruses. ## **LIPIDS:** - Lipids are esters of fatty acids and alcohol. - They have a low molecular weight of less than 800 Dalton. - They are insoluble in water. ##**TYPES OF LIPIDS:** - Lipids can be broadly classified into 3 categories: ### **1) Simple Lipids:** - They are lipids made up of fatty acids and alcohol only. - These are lipids made up of fatty acids and an alcohol. - The R groups in fatty acids could be made up of to C₁₆-C₁₈, like palmitic acid has 16 carbon atoms (CH₃-(CH₂)₁₄-COOH), and arachidonic acids has 20 carbon atoms (CH₃-(CH₂)₄-(CH=CH-CH₂)₄-(CH₂)₃-COOH). ### **2) Conjugated Lipids:** - These are lipids containing some additional groups with fatty acids and alcohol. **Examples:** #### **1) Phospholipids:** - Made up of fatty acids, glycerol, and a phosphate group. - It is also called Lecithin. #### **2) Glycolipids:** - FA + Alcohol + Carbohydrate. ### **3) Derived Lipids:** - Lipid-like substances which are derived from lipids. - They don't have any structural similarities with lipids, but they can be classified together because of their hydrophobic nature. - Example: cholesterol. ## **ENZYMES:** - Enzymes are biological catalysts which catalyse biochemical reaction in living cells - Most enzymes are made up of proteins except: ribozyme (which is a nucleic acid). - Enzymes are proteins in their 3⁰ structure. - Each enzyme catalyses a specific biochemical reaction only. - It is because of specific configuration of active sites of the enzymes, which bind to specific substrate only (lock & key). ## **Active site:** - It is a pocket of an enzyme into which a particular substrate fits ## **ENZYMES Vs INORGANIC CATALYST:** 1. **It catalyses only specific reaction** 2. **Enzymes get denatured at high temperature (denatured)** 3. **They are sensitive to changes of pH of the medium.** 4. **They can work efficiently at high temperature and pressure.** 5. **They do not have any effect on pH change.** ## **RATE OF REACTION:** - The rate of a reaction refers to the amount of product formed per unit time. - **Rate = Rate of change of product.** - **Catalysed reaction** proceed at rates higher than **uncatalysed reactions**. ### **Example:** **CO₂ + H₂O > H₂CO₃** - **Carbonic anhydrase** &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**Carbonic acid** - **Without enzyme: Rate = 200 molecules/sec.** - **With Carbonic Anhydrase: Rate = 600000 molecules/sec.** ## **HOW DO ENZYMES ENHANCE RATE OF REACTION?** - What is activation energy? - Most of the reactant molecules have to supply activation energy without enzyme during a chemical reaction. - Chemical reaction do not start automatically because the activation energy barrier to become active. - Therefore, an external supply of energy is needed for starting of the chemical reaction. - This energy is called activation energy. - The minimum amount of energy substrate must posses to convert into product is called the activation energy - Enzyme enhances speed of chemical reaction by lowering the activation energy. ## **CATALYTIC CYCLE OF AN ENZYME** 1. **Enzyme is available with free active site** 2. **The substrate enters the active site, which enfolds the substrate with an induced fit.** 3. **The substrate is converted into product.** 4. **Product are released** ## **The catalytic cycle of an enzyme action can be described in the following steps:** 1. First the substrate binds to the active site of the enzyme, fitting into the active site. 2. The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate. 3. The active site of the enzyme now breaks the chemical bonds of the substrate, and the new **enzyme-product complex** is formed. 4. The enzyme releases the products of the reaction and the free enzyme is available for the next cycle ## **FACTORS AFFECTING ENZYME ACTIVITY:** **1) Temperature:** - Enzyme shows highest activity at optimum temperature. - At first with the increase in temperature, enzyme activity increases but after a limit, the activity of enzymes decreases again. - This is due to denaturation of enzymes at high temp. ## **2) pH:** - Enzymes shows highest activity at optimum pH only. - Below and above the optimum pH, enzymes activity decreases. ## **3) Substrate Concentration** - The rate of reaction increases with substrate concentration till it reaches maximum velocity (V_max). - The substrate concentration in which the corresponding rate of reaction attains ½V_max is called Michaelis constant (K_m). ## **4) Rate of reaction increases with substrate concentration till it reaches maximum velocity (V_max).** ## **5) Presence of inhibitor:** - When the binding of a chemical shuts off the enzyme activity, the process is called **inhibition** and the chemical is called an inhibitor. - There are two types of enzyme inhibition: **1) Competitive Inhibition:** - Inhibitor closely resembles the substrate in molecular structure, and inhibits enzyme activity by binding at the active site of the enzyme. **Example: Inhibition of succinate dehydrogenase by malonate.** **2) Non- competitive Inhibition:** - In this type of inhibition, activity is done by the binding of an inhibitor at a site other than the active site (allosteric site). - The inhibitor doesn't resemble the substrate. **Example:** Inhibition of cytochrome oxidase by cyanide. ## **CLASSIFICATION OF ENZYMES:** ### **1) Oxidoreductases:** - This group of enzymes catalyse oxidation-reduction reaction. - They eliminate O₂ from one substrate and transfer it to another. **Example: A + 2e^- > A⁺² + 2e^- (reduced oxidised)** ### **2) Transferases:** - It catalyses transfer of a group between a pair of substrates. **Example: S + G > S' + G'** ### **3) Hydrolases:** - It catalyzes hydrolysis of ester, ether, peptide, glycosidic bond etc. **Example: X - Y > X + Y** ### **4) Lyases:** - It catalyzes removal of groups from substrates by mechanism other than hydrolysis. - C - C > C= C + X - Y ### **5) Isomerases:** - It catalyses isomerisation reaction. ### **6) Ligases:** - It catalyses linking together of two compounds. **Co_factors:** - These are non-protein constituents found attached to the enzyme to make it catalytically active. - The protein portion of enzyme is called apoenzyme. - Apoenzyme and co-factor together forms holoenzyme. - **Holoenzyme = Apoenzyme + Co-factor** - **Co-factor** can be divided into 3 categories:&#x20; ### **1) Prosthetic Group:** - Organic compounds (co-factor) tightly bound to the apoenzyme. - **Example:** Peroxidase and Catalase has heme as their prosthetic group. ### **2) Co-enzyme:** - These are organic compounds loosely bind with the enzyme. - **Example:** Vitamins, NAD, etc. ### **3) Metal ions:** - These are metals that remain associated with the apoenzyme to make it catalytically active. ## **NOTES:** - **Reaction with enzyme & without inhibitor:** <br> <br> <img src="https://i.imgur.com/8n41o4j.png" alt="Rate of Reaction Chart" width="400" height="200"> <br> <br>