Biochemistry and the Chemistry of Life: A Comprehensive Guide

Introduction to Biochemistry and the Chemistry of Life

• Definition of Biochemistry:     * The study of chemical substances and vital processes occurring in living organisms.     * The chemical composition of a particular living system or biological substances.

• Chemistry of Life Components:     * All substances are made of atoms.     * Living organisms are composed of various elements and compounds, categorized as follows:         * Inorganic Compounds:             * Water ($H_2O$).             * Minerals (Mineral salts).         * Organic Compounds:             * Carbohydrates.             * Proteins.             * Lipids (Fats).             * Vitamins.             * Nucleic Acids.

Basic Biological Units and Processes

• Hierarchy of Life:     * Chemical compounds are organized in complex ways to form cells, which are the basic units of life.     * Plant and animal cells serve as the basic structural and functional units of organisms.

• The Seven Basic Characteristics/Processes of Life (7 LP):     1. Movement (Locomotion).     2. Respiration.     3. Stimuli-response (Sensitivity).     4. Growth.     5. Reproduction.     6. Excretion.     7. Nutrition.

• Definitions of Matter Units:     * Atom: The smallest unit of matter (living or non-living) that can take part in chemical reactions.     * Element: A pure substance made up of the same simple substance (atoms) that cannot be broken down further.     * Compound: A pure substance made of different simpler substances (elements) that have chemically bonded in a fixed ratio.     * Molecule: Two or more atoms that have chemically bonded.

• Levels of Organization:     * Cell: The smallest unit of life containing cellular inclusions known as organelles (sub-cellular components).     * Tissue: A group of similarly differentiated or specialized cells that perform a common function.     * Organ: A group of differentiated or specialized tissues, each performing its own function, but together performing a larger common function.     * Systems: Composed of different organs working together to perform a common function; they form sub-systems within an organism.     * Organism: Composed of systems of organs working together to sustain life and carry out the seven life processes.

Inorganic vs. Organic Compounds

• Inorganic Compounds:     * Definition: Compounds that do not contain Carbon ($C$), with exceptions like Carbon Dioxide ($CO_2$), Carbon Monoxide ($CO$), and Carbonates ($-CO_3$).     * Characteristics: Generally not produced by living organisms (e.g., water, gases, minerals) but can be formed during biochemical reactions as waste products.

• Organic Compounds:     * Definition: Compounds containing Carbon ($C$) and Hydrogen ($H$), often called hydrocarbons.     * Composition: Primarily composed of Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$), but may also include Nitrogen ($N$), Phosphorus ($P$), and Sulphur ($S$) (Acronym: NCHOPS).     * Characteristics: Produced by living organisms; they constitute the building blocks of cells.

Water ($H_2O$) as a Vital Inorganic Compound

• Occurrence and Structure:     * Most important inorganic compound for all life.     * Exists naturally in three states: Solid (Ice on mountains), Liquid (Rivers, lakes, oceans), and Gas (Water vapor in the atmosphere).     * Molecule consists of one Oxygen ($O$) atom and two Hydrogen ($H$) atoms bonded by polar covalent bonds.

• Biological Composition levels:     * $70\text{--}95\%$ of cells consist of water.     * $85\%$ of protoplasm is water.     * $75\%$ of plant and animal bodies is water.     * $60\text{--}75\%$ of human body mass is water.

• Functions of Water:     1. Solvent: Vital for ionization; dissolves organic and inorganic compounds. Allows roots to absorb mineral salts from soil. Gas exchange (dissolving $O_2$ and $CO_2$ before cell entry). Excretion of metabolic wastes (urea in sweat/urine).     2. Medium for Chemical Reactions: Reactions in cells occur in water, including enzymatic actions. Essential for photosynthesis.     3. Reagent during Hydrolysis: Water is added to break down large organic compounds (polymers) into smaller ones (monomers) during digestion.     4. Transporting Agent: Moves digested nutrients, waste products, gases ($CO_2$ and $O_2$), and secretions in the blood. Moves minerals via xylem and phloem in plants.     5. Lubricant: Fluid in mucous membranes eases chewing and swallowing. Watery fluids around eyeballs and joints prevent friction and act as shock absorbers.     6. Temperature Regulation: Sweat evaporation cools animals. Transpiration cools plants and drives water absorption.     7. Shape, Rigidity, and Pliability: Provides hydrostatic skeletons for animals like earthworms and jellyfish. Creates turgor pressure (turgidity) in plant vacuoles to keep cells firm. Keeps tissues soft and pliable.     8. Habitat: Provides a living environment for aquatic organisms.

• Unique Physical Properties:     * Expands upon freezing ($0\,^\circ\text{C}$), causing ice to float.     * Densest at $4\,^\circ\text{C}$. Bottom-up freezing is prevented, allowing aquatic survival.     * High surface tension and strong attraction between molecules leads to capillarity (water rising in tubes).     * High specific heat capacity: Absorbs large quantities of heat without rapid temperature changes.

Inorganic Minerals and Mineral Salts

• Minerals are obtained in salt forms (e.g., Sodium from Sodium Chloride, $NaCl$).

• Classification:     * Macro-elements: Required in large quantities (e.g., $N, Ca, Na, K, S, P, Mg$).     * Micro-elements (Trace elements): Required in small quantities (e.g., $Fe, I, Zn, Cu, Mn, Se$).

• Roles of Macro-elements:     * Nitrogen ($N$):         * Animals: Protein synthesis; component of enzymes, amino acids, and nucleic acids ($DNA$, $RNA$). Deficiency: Kwashiorkor in children, retarded growth.         * Plants: Chlorophyll synthesis; component of amino acids and nucleic acids. Deficiency: Chlorosis (yellowing) in older leaves; reduced growth.     * Calcium ($Ca$):         * Animals: Strong teeth/bones; blood clotting (coagulation); muscle contraction/nerve impulses; membrane permeability. Deficiency: Rickets, osteomalacia, osteoporosis.         * Plants: Component of middle lamella in cell walls; activates enzymes. Deficiency: Death of shoots, chlorosis of young leaves.     * Sodium ($Na$):         * Animals: Osmotic balance; $HCl$ secretion in stomach; nerve/kidney function. Deficiency: Muscle cramps.         * Plants: (Micro-element for plants) Maintains osmotic balance. Deficiency: Reduced growth.     * Potassium ($K$):         * Animals: Blood pressure and heart rhythm; water balance. Deficiency: Muscle cramps, lung failure.         * Plants: Photosynthesis; protein synthesis; stomata regulation. Deficiency: Drought resistance loss, brown leaf margins.     * Phosphorus ($P$):         * Animals: Teeth/bones; component of $ATP$, $DNA$, $RNA$, and phospholipids. Deficiency: Malfunctioning muscles.         * Plants: Cell membrane component; $ATP$ production; promotes root/fruit development. Deficiency: Stunted growth, purple leaves.     * Magnesium ($Mg$):         * Animals: Bone/teeth formation; enzyme activator. Deficiency: Muscle cramps.         * Plants: Core component of chlorophyll. Deficiency: Chlorosis (bottom-up yellowing).

• Roles of Micro-elements:     * Iron ($Fe$):         * Animals: Synthesis of haemoglobin in red blood cells. Deficiency: Anaemia.         * Plants: Chlorophyll formation; carrier in photosynthesis. Deficiency: Chlorosis.     * Iodine ($I$):         * Animals: Formation of thyroxin in the thyroid gland. Deficiency: Cretinism (children), Goitre (adults).

Fertilisers and Eutrophication

• Fertilisers: Added to counteract mineral deficiencies in soil.     * Natural: Compost, sewage sludge, animal manure.     * Artificial: NPK fertilisers containing Nitrogen ($N$) for growth, Phosphorus ($P$) for establishment, and Potassium ($K$) for stress tolerance.

• The Eutrophication Process:     1. Nutrient Load Up: Excessive fertilisers are leached from soil by rain into water bodies.     2. Plants Flourish: Pollutants cause aquatic growth of algae and duckweed.     3. Algal Bloom: A thick layer of algae prevents sunlight from reaching bottom plants, leading to plant death and reduced oxygen from photosynthesis.     4. Decomposition: Saprophytic bacteria and fungi decompose dead matter, consuming remaining oxygen ($O_2$) in the water.     5. Death of Ecosystem: Oxygen levels become too low for fish and other organisms, leading to total collapse of the aquatic ecosystem.

Organic Compounds: Carbohydrates

• General Characteristics:     * Molecules contain Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$).     * Ratio of $H$ to $O$ is always $2:1$. General formula ratio: $1:2:1$ ($C_n H_{2n} O_n$). Example: Glucose is $C_6H_{12}O_6$.     * Building blocks are single-ring units called saccharides (hexagonal shape).

• Types of Carbohydrates:     1. Monosaccharides (Simple Sugars): Single ring. Soluble and sweet.         * Glucose ($Gl$): Primary energy source.         * Fructose ($Fr$): Fruit sugar.         * Galactose ($Gal$): Milk sugar component.     2. Disaccharides (Double Sugars): Two rings joined through condensation (removal of $H_2O$). Soluble and sweet.         * $Glucose + Glucose \rightarrow Maltose + H_2O$ (Enzyme: maltase).         * $Glucose + Fructose \rightarrow Sucrose + H_2O$ (Enzyme: sucrase).         * $Glucose + Galactose \rightarrow Lactose + H_2O$ (Enzyme: lactase).     3. Polysaccharides (Complex Sugars): Chains of many rings. Insoluble and tasteless.         * Starch: Energy storage in plants. Broken down by amylase.         * Glycogen: More extensively branched than starch. Energy storage in animal liver and muscles. Regulated by glucagon.         * Cellulose: Structural component of plant cell walls. Indigestible fiber for humans (no specific enzyme).

• Reactions:     * Condensation: Linking monomers to form polymers by removing water.     * Hydrolysis: Breaking down polymers into monomers by adding water.

• Tests for Carbohydrates:     * Glucose/Simple Sugars: Benedict’s Solution or Fehling’s A and B. Positive result: Brick red color after heating.     * Starch: Iodine solution. Positive result: Blue-black color.     * Cellulose: Schultz’s Solution. Positive result: Purple color.

Supplemental Topic: Determining the Age of Fossils

• Relative Dating:     * Determines relative age by comparing fossils to known strata or other fossils in the fossil record.     * Stratigraphic dating: Based on the sequence of species in rock layers.     * Fluorine Analysis: Compares accumulated fluorine in bones as they fossilize.
• Radiometric Dating: Uses radioactive decay to determine absolute age (mentioned as the second method).