Biomolecules (NEET Class 11)

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1. Introduction to Biomolecules Living organisms have chemical compounds called biomolecules . Quantitative Analysis of Living Tissue: Wet Weight: Total weight of the living tissue. Dry Weight: Weight after drying the tissue to remove all water and $CO_2$. Ash Analysis: Burning dried tissue to oxidize carbon compounds, leaving inorganic elements (ash). Elemental Analysis: Hydrogen, Carbon, Nitrogen, Sulphur are more abundant in living matter than in earth's crust. Oxygen is highly abundant in both living organisms and the earth's crust. Silicon is abundant in earth's crust but negligible in living matter. Chemical Analysis (Acid Extraction): Grind living tissue in trichloroacetic acid ($CCl_3COOH$). Filter through cheeseloth/cotton. Acid-soluble pool (filtrate): Contains micromolecules (MW < 1000 Da), e.g., amino acids, sugars, nucleotides. It represents roughly the cytoplasmic composition . Also contains inorganic ions like $Na^+, K^+, Ca^{2+}, Mg^{2+}, Cl^-, PO_4^{3-}, SO_4^{2-}$. Acid-insoluble fraction (retentate): Contains macromolecules (MW > 1000 Da), e.g., proteins, nucleic acids, polysaccharides. This fraction mainly includes organelles and cell membrane components. Exception: Lipids (MW < 800 Da) are found in the acid-insoluble fraction because they aggregate into vesicles during grinding and precipitation. Composition of a Cell (% of total cellular mass): Water (70–90%) > Proteins (10–15%) > Nucleic acids (5–7%) > Carbohydrates (3%) > Lipids (2%) > Ions (1%) (Trick: WP nakli) Primary vs. Secondary Metabolites: Basis Primary Metabolites Secondary Metabolites Occurrence Present in all living cells Present mainly in plants, fungi, microbes Role Direct role in growth, development & metabolism No direct role in growth and development Involvement Involved in physiological processes Involved in ecological interactions Examples / Types Amino acids, sugars, nucleotides, lipids Pigments, Alkaloids, Terpenoids, Essential oils, Toxins, Lectins, Drugs, Polymeric substances Importance Essential for life processes Important for defence, attraction, signalling, survival Examples of Metabolites: Primary: Amino acids, sugars, nucleotides, lipids Secondary: Pigments – Carotenoids, Anthocyanins; Alkaloids – Morphine, Codeine; Terpenoids – Monoterpenes, Diterpenes; Essential oils – Lemongrass oil; Toxins – Abrin, Ricin; Lectins – Concanavalin A; Drugs – Vinblastin, Curcumin; Polymeric substances – Rubber, gums, cellulose 2. Amino Acids Organic compounds containing an amino group $(-\text{NH}_2)$ and a carboxyl group $(-\text{COOH})$ on the same carbon (alpha-carbon). Also have a hydrogen atom and a variable group 'R' attached to the alpha-carbon. Types based on 'R' group: Glycine: R = H (simplest) Alanine: R = Methyl group ($-CH_3$) Serine: R = Hydroxy methyl group ($-CH_2OH$) Acidic amino acids: e.g., glutamic acid Basic amino acids: e.g., lysine Neutral amino acids: e.g., valine Aromatic amino acids: tyrosine, phenylalanine, tryptophan. Sulfur-containing AAs: Methionine, Cysteine. Essential Amino Acids: Cannot be synthesized by the body, must be obtained from diet (e.g., Lysine, Leucine, Isoleucine, Valine). Non-essential Amino Acids: Can be synthesized by the body. Amphoteric Nature: Act as both acid and base. Structure of amino acids changes with pH. In solution, amino acids exist as: Cationic form Zwitterionic form (dipolar ion) → most stable Anionic form 3. Proteins Polymers of amino acids linked by peptide bonds . There are 20 types of amino acids that make up proteins. Peptide bond: Formed by dehydration reaction between $-\text{COOH}$ of one amino acid and $-\text{NH}_2$ of another. Each protein is a heteropolymer (not homopolymer) as it contains different types of amino acids. Structure of Proteins: Primary: Linear sequence of amino acids. Written from N-terminal ($-\text{NH}_2$) to C-terminal ($-\text{COOH}$) . Determined by genetic information. Secondary: Folding of the polypeptide chain into specific shapes. $\alpha$-helix: Right-handed coiled structure. $\beta$-pleated sheet: Folded, sheet-like structure. Held by hydrogen bonds. Tertiary: Overall 3D shape of a polypeptide chain. Critical for biological activity. Stabilized by various bonds (H-bonds, ionic, disulfide, hydrophobic interactions). Quaternary: Arrangement of multiple polypeptide subunits (e.g., Hemoglobin has 4 subunits). Functions & Examples: Enzymes, transport (Hemoglobin), hormones (Insulin), antibodies, receptors. Collagen: Most abundant protein in animal world; functions as intercellular ground substance . RuBisCO: Most abundant protein in the whole biosphere. GLUT-4: Enables glucose transport into cells. 4. Polysaccharides (Carbohydrates) Polysaccharides are polymers of monosaccharide units linked by glycosidic bonds (formed by dehydration). In a polysaccharide chain: The left end is called the non-reducing end . The right end is called the reducing end . Types of Polysaccharides: Starch: Storage polysaccharide in plants. Homopolymer of $\alpha$-glucose. Forms helical secondary structures. These helices can hold $I_2$ molecules, giving a blue colour with iodine. Glycogen: Storage polysaccharide in animals (liver and muscles). Highly branched homopolymer of $\alpha$-glucose. Cellulose: Major component of plant cell walls. Homopolymer of $\beta$-glucose. Does not form complex helices, hence cannot hold $I_2$. Paper made from plant pulp and cotton fibre is primarily composed of cellulose. Inulin: A homopolymer of fructose. Polysaccharides from Modified Sugars: Amino sugars: Sugars in which an $-\text{OH}$ group is replaced by an $-\text{NH}_2$ group. Examples: Glucosamine, N-acetyl galactosamine. Chitin: A chemically complex homopolymer of N-acetyl glucosamine (a modified sugar). Found in the exoskeleton of arthropods and fungal cell walls. Carbohydrate Classification: Monosaccharides: Glucose, Fructose, Ribose, Galactose. Disaccharides: Sucrose = Glucose + Fructose Lactose = Glucose + Galactose Maltose = Glucose + Glucose 5. Lipids Fatty Acids: Carboxyl group + R group. Saturated: No double bonds (e.g., Palmitic acid - 16C). Unsaturated: Double bonds (e.g., Arachidonic acid - 20C). Glycerol: Trihydroxy propane. Triglycerides (Fats & Oils): Glycerol + 3 fatty acids. Fats: Solid, saturated FAs. Oils: Liquid, unsaturated FAs (e.g., Gingelly oil - low mp). Phospholipid: e.g., Lecithin. Neural tissues contain more complex lipids. Cholesterol: Steroid, hormone precursor. 6. Nucleic Acids Polymers of nucleotides. Nucleotide: Pentose sugar + Nitrogenous base + Phosphate. Nucleoside: Pentose sugar + Nitrogenous base. Bonds: N-glycosidic bond: Base to pentose sugar. Phosphoester bond: Phosphate to pentose sugar. Phosphodiester bond: Links 3′-OH of one sugar to 5′-phosphate of next nucleotide. Nitrogenous Bases: Purines: Adenine (A), Guanine (G) (double ring). Pyrimidines: Cytosine (C), Thymine (T), Uracil (U) (single ring). Pentose Sugars: Ribose (RNA), Deoxyribose (DNA). Common Nucleosides and Nucleotides: Adenine: Adenosine, Adenylic acid Guanine: Guanosine, Guanylic acid Cytosine: Cytidine, Cytidylic acid Thymine: Deoxythymidine, Deoxythymidylic acid Uracil: Uridine, Uridylic acid DNA Secondary Structure (B-DNA - Watson-Crick): Double helix, antiparallel strands. Sugar-phosphate backbone, bases inwards. Bases pair via hydrogen bonds: A=T (2 H-bonds), G≡C (3 H-bonds). One full turn: 34 Å pitch , 10 base pairs (bp) . Distance between two consecutive base pairs: 3.4 Å . Each base pair turn: 36° . 7. Enzymes Almost all enzymes are proteins. Some RNA molecules also act as enzymes (called ribozymes ). Enzymes have primary, secondary and tertiary structure. Tertiary structure creates crevices or pockets called the active site . Enzymes are highly specific and very efficient. Unlike inorganic catalysts, enzymes work at normal temperature and pressure. Rate of physical and chemical processes are influenced by temperature among other factors. Rate doubles or decreases by half for every 10°C change in either direction. Enzyme-catalysed reactions are much faster than uncatalysed ones. Example: $CO_2 + H_2O \rightleftharpoons H_2CO_3$ (catalyzed by carbonic anhydrase). Without enzyme: ~200 molecules/hour. With enzyme: ~600,000 molecules/second. Rate increased by ~10 million times. Reaction sequence: $E + S \rightleftharpoons ES \rightleftharpoons EP \rightleftharpoons E + P$ ES complex is short-lived but essential. Activation Energy: Enzyme does not change $\Delta G$, only lowers energy barrier. Factors Affecting Enzyme Activity: (a) Temperature: Enzymes work best at optimum temperature. Low temperature $\rightarrow$ inactive but not destroyed. High temperature $\rightarrow$ denaturation. (b) pH: Each enzyme has optimum pH. Activity decreases above or below optimum. (c) Substrate Concentration: Rate increases with substrate concentration. Reaches $V_{max}$ when enzyme is saturated. $K_m$ = substrate concentration at $1/2 V_{max}$. Enzyme Inhibition: Inhibitor reduces enzyme activity. Competitive inhibitor: Resembles substrate. Competes for active site. Example: Malonate inhibits succinic dehydrogenase. Used in control of bacterial pathogens. Classification of Enzymes (6 Classes): (each with 4-13 subclasses and named accordingly by a four-digit number). Oxidoreductases: Catalyze oxidation-reduction reactions. Transferases: Transfer of groups (other than hydrogen) between a pair of substrates. Hydrolases: Catalyze hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide, or P-N bonds. Lyases: Removal of groups without hydrolysis, leaving double bonds. Isomerases: Catalyze interconversion of optical, geometric, or positional isomers. Ligases (Synthetases): Joining of two molecules using ATP (e.g., C-S, C-O, C-N bonds). Cofactors: Non-protein part required for enzyme activity. Protein part alone = apoenzyme . Apoenzyme + cofactor = holoenzyme . Types of Cofactors: Prosthetic group: Tightly bound. Example: Haem in catalase and peroxidase. Coenzyme: Loosely bound to the apoenzyme. Often vitamins. Example: NAD, NADP contain the vitamin- niacin. Metal ions: Form coordination bonds with side chains at the active site and at the same time form one or more coordination bonds with the substrate. Example: $Zn^{2+}$ in carboxypeptidase. Removing cofactor $\rightarrow$ enzyme becomes inactive. 8. The Living State & Metabolism Living cells contain thousands of metabolites at specific concentrations. Example: Blood glucose level: 4.2–6.1 mmol/L. Example: Hormones: nanograms/mL. Living systems maintain a steady state with constant biomolecule concentrations despite continuous metabolic flux. This steady state prevents equilibrium by continuous energy input. Biomolecules show continuous turnover (constant breaking + synthesis). Majority of living reactions do not occur in isolation and are always converted in linked reactions called metabolic pathways . Metabolic Pathways can be linear, circular, or criss-cross each other. Metabolite Flow: Has a definite rate & direction, representing the dynamic state . All reactions are enzyme-catalysed ; there is no uncatalysed reaction in living cells. Metabolic Pathways: Anabolic pathways: Build up complex molecules from simpler ones, consume energy. Example: amino acids $\rightarrow$ proteins. Example: acetic acid $\rightarrow$ cholesterol. Catabolic pathways: Break down complex molecules into simpler ones, release energy. Example: glucose $\rightarrow$ lactic acid in skeletal muscles. ATP (Adenosine Triphosphate): Energy currency of the cell. Stores energy in chemical bonds. Used for: Biosynthesis. Osmotic work (to create/maintain the gradient, not for water flow). Mechanical work.