Biology: Class 11 — Chapter 9: Chapter 9: Biomolecules

To analyze the organic chemical composition of living tissue, the tissue (e.g., vegetable or liver) is ground in trichloroacetic acid ($Cl_3CCOOH$) using a mortar and pestle to form a thick slurry. Straining this slurry through cheesecloth yields two distinct fractions:

• Acid-soluble pool (Filtrate): Contains thousands of organic compounds with molecular weights ranging from 18 to approximately 800 Daltons (Da). This represents the cytoplasmic composition.
• Acid-insoluble fraction (Retentate): Contains polymeric macromolecules (proteins, polysaccharides, nucleic acids) and lipids.

Elemental analysis of living tissue reveals the presence of hydrogen, oxygen, chlorine, carbon, etc. A comparison shows that the relative abundance of carbon and hydrogen is higher in living organisms than in the Earth's crust.

To analyze inorganic elements and compounds, a destructive experiment is performed: living tissue is weighed (wet weight), dried to evaporate all water (dry weight), and fully burnt. The remaining ash contains inorganic elements and compounds:

• Inorganic Elements: Calcium ($Ca^{2+}$), Magnesium ($Mg^{2+}$), Sodium ($Na^+$), Potassium ($K^+$).
• Inorganic Compounds: Phosphate ($PO_4^{3-}$), Sulphate ($SO_4^{2-}$), Water ($H_2O$), Sodium Chloride ($NaCl$), Calcium Carbonate ($CaCO_3$).

Amino acids are organic compounds containing an amino group ($-NH_2$) and an acidic carboxyl group ($-COOH$) as substituents on the same carbon ($\alpha$-carbon). They are substituted methanes with four substituent groups occupying the valency positions: hydrogen, carboxyl group, amino group, and a variable R group.

• Glycine: R group is Hydrogen ($-H$).
• Alanine: R group is a Methyl group ($-CH_3$).
• Serine: R group is a Hydroxy-methyl group ($-CH_2OH$).
• Zwitterionic Form: Due to the ionizable nature of $-NH_2$ and $-COOH$ groups, the structure of amino acids changes in solutions of different pH, existing as a dipolar ion.

Lipids are generally water-insoluble organic molecules. They can be simple fatty acids, glycerol, or complex conjugated structures:

• Fatty Acids: Contain a carboxyl group attached to an R group (ranging from 1 to 19 carbons). Examples include palmitic acid (16 carbons) and arachidonic acid (20 carbons). They can be saturated (no double bonds) or unsaturated (one or more $C=C$ double bonds).
• Glycerol: Trihydroxy propane. Many lipids have fatty acids esterified with glycerol, forming monoglycerides, diglycerides, and triglycerides.
• Phospholipids: Lipids containing phosphorus and a phosphorylated organic compound, such as lecithin, which is a major component of cell membranes.

Biomolecules can be classified based on their physiological roles and distribution in organisms:

• Primary Metabolites: Have identifiable functions and play known roles in normal physiological processes (e.g., amino acids, sugars, lipids, nucleotides).
• Secondary Metabolites: Produced primarily by plants, fungi, and microbes. Their specific physiological roles in the host organisms are often not fully understood, but many have ecological importance or economic utility for human welfare.

• Pigments: Carotenoids, Anthocyanins.
• Alkaloids: Morphine, Codeine.
• Terpenoids: Monoterpenes, Diterpenes.
• Essential Oils: Lemon grass oil.
• Toxins: Abrin, Ricin.
• Lectins: Concanavalin A.
• Drugs: Vinblastin, Curcumin.
• Polymeric Substances: Rubber, Gums, Cellulose.

Biomolecules are divided into two categories based on molecular weight and solubility:

• Biomicro-molecules: Found in the acid-soluble pool, with molecular weights ranging from 18 to 800 Da.
• Biomacromolecules: Found in the acid-insoluble fraction, with molecular weights of 10,000 Da and above. These include proteins, polysaccharides, and nucleic acids.

Although lipids have molecular weights not exceeding 800 Da (making them micromolecules), they are recovered in the acid-insoluble macromolecular fraction. This is because lipids are arranged in structures like cell membranes. When tissue is ground, these membranes break into water-insoluble vesicles that get filtered out with the macromolecular retentate.

Proteins are polypeptides. They are linear chains of amino acids linked by peptide bonds. Every protein is a heteropolymer (composed of different types of amino acids) rather than a homopolymer.

• There are 20 types of amino acids that constitute proteins.
• Essential Amino Acids: Cannot be synthesized by the body and must be supplied through the diet.
• Non-essential Amino Acids: Can be synthesized by the body.

• Collagen: Intercellular ground substance; the most abundant protein in the animal world.
• RuBisCO: Ribulose bisphosphate Carboxylase-Oxygenase; the most abundant protein in the entire biosphere.
• Trypsin: Digestive enzyme.
• Insulin: Peptide hormone regulating glucose levels.
• Antibody: Fights infectious agents.
• GLUT-4: Enables glucose transport into cells.

Polysaccharides are long chains of monosaccharides linked together. They serve as structural components or energy stores:

• Cellulose: A homopolymer of glucose that forms plant cell walls. It is non-helical and cannot hold iodine.
• Starch: A helical homopolymer of glucose that serves as an energy store in plants. Its helical secondary structure can hold iodine molecules ($I_2$), forming a blue-coloured complex.
• Glycogen: A highly branched glucose polymer serving as an energy store in animals. The right end is the reducing end, and the left end is the non-reducing end.
• Inulin: A polymer of fructose.
• Chitin: A complex homopolymer of chemically modified amino-sugars (like N-acetyl glucosamine) forming the exoskeleton of arthropods.

Nucleic acids (DNA and RNA) are polynucleotides found in the acid-insoluble fraction. They function as genetic material. A single nucleotide consists of three chemically distinct components:

1. Heterocyclic Nitrogenous Base: Purines (Adenine, Guanine) or Pyrimidines (Cytosine, Uracil, Thymine).
2. Pentose Sugar: Ribose (in RNA) or 2'-deoxyribose (in DNA).
3. Phosphate Group: Phosphoric acid esterified to the sugar.

• Nucleoside: Nitrogenous base + Sugar (e.g., Adenosine, Guanosine, Thymidine, Uridine, Cytidine).
• Nucleotide: Nitrogenous base + Sugar + Phosphate (e.g., Adenylic acid, Thymidylic acid, Guanylic acid).

Biologists describe protein structure at four hierarchical levels:

• Primary Structure: The linear sequence of amino acids. The left end is the first amino acid (N-terminal), and the right end is the last amino acid (C-terminal).
• Secondary Structure: Local folding of the polypeptide chain, primarily into a right-handed $\alpha$-helix or $\beta$-pleated sheet, stabilized by hydrogen bonds.
• Tertiary Structure: The folding of the polypeptide chain upon itself like a hollow woolen ball, creating a 3D conformation. This structure is stabilized by hydrogen bonds, disulfide bonds, and hydrophobic interactions, and is absolutely necessary for biological activity.
• Quaternary Structure: The spatial arrangement of multiple polypeptide subunits. For example, adult human haemoglobin consists of 4 subunits ($2\alpha$ and $2\beta$ chains).

Almost all enzymes are proteins. Some nucleic acids that behave like enzymes are called ribozymes. An enzyme has a specific pocket or crevice called the active site, into which the substrate fits to undergo catalysis.

• Enzymes are highly specific and operate at high rates.
• Unlike inorganic catalysts, enzymes are denatured and damaged at high temperatures (usually above 40°C), except for those isolated from thermophilic organisms (stable up to 80°-90°C).

Enzymes accelerate chemical reactions by lowering the activation energy barrier required to transition the substrate ($S$) into the product ($P$).

• The substrate binds to the active site, forming a transient, highly reactive enzyme-substrate (ES) complex: $$E + S \rightleftharpoons ES \rightarrow EP \rightarrow E + P$$
• During the ES state, the substrate is forced into a transition state structure where chemical bonds are broken and new ones are formed.

• Temperature and pH: Enzymes function within a narrow range. Activity is maximum at optimum temperature and pH, and declines above or below these values. Low temperature preserves enzymes in an inactive state, while high temperature denatures them.
• Substrate Concentration: Velocity of reaction increases with substrate concentration until it reaches a maximum velocity ($V_{max}$), where all enzyme active sites are saturated.
• Inhibition: Specific chemicals can bind to the enzyme and shut off its activity. In competitive inhibition, the inhibitor closely resembles the substrate in structure and competes for the active site (e.g., inhibition of succinic dehydrogenase by malonate).

Enzymes are divided into 6 major classes:

1. Oxidoreductases/Dehydrogenases: Catalyse oxidoreduction between two substrates.
2. Transferases: Catalyse transfer of a group (other than hydrogen) between a pair of substrates.
3. Hydrolases: Catalyse hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide, or P-N bonds.
4. Lyases: Catalyse removal of groups from substrates by mechanisms other than hydrolysis, leaving double bonds.
5. Isomerases: Catalyse inter-conversion of optical, geometric, or positional isomers.
6. Ligases: Catalyse the linking together of two compounds (e.g., joining C-O, C-S, C-N, or P-O bonds).

Many enzymes require non-protein constituents called co-factors bound to the protein portion (apoenzyme) to become catalytically active:

• Prosthetic Groups: Organic compounds tightly bound to the apoenzyme (e.g., haem in peroxidase and catalase).
• Co-enzymes: Transiently bound organic compounds, often derived from vitamins (e.g., NAD and NADP contain niacin).
• Metal Ions: Form coordination bonds with the active site and substrate (e.g., Zinc is a co-factor for carboxypeptidase).