Unit 4: Biomolecules — Interactive Notes
Living organisms are made up of about 25 chemical elements, of which C, H, O and N make up 96% of living mass. Most of the molecules in living organisms are organic (carbon-based).
Most organic molecules are large in size — biologists call them macromolecules. Many macromolecules are in the form of polymers. A polymer is a molecule consisting of many identical molecular units, called monomers. Important macromolecules like carbohydrates, proteins, and nucleic acids are polymers of simple monomers i.e., sugars, amino acids and nucleotides respectively.
Metabolism: All the chemical reactions taking place within a cell are collectively called metabolism — either anabolism (simpler → complex substances) or catabolism (complex → simpler molecules).
Functional group: Organic molecules have a carbon-based core with special groups of atoms attached, called functional groups (e.g. OH, CO, COOH, NH₂). Most biochemical reactions involve the transfer of a functional group from one molecule to another, or the breaking of a carbon-carbon bond.
Importance of carbon: Carbon is the basic element of organic molecules — tetravalent, reacting with many elements like H, O, N, P and S. The C-H bond is a potential source of chemical energy for cellular activities. Carbon-oxygen association in glycosidic linkages stabilizes complex carbohydrates. Carbon combines with nitrogen in amino acid linkages to form peptide bonds and proteins.
1. Covalent Bonds: Form when two atoms share electrons.
Significance: Found in organic molecules like proteins and nucleic acids, providing stability.
2. Ionic Bonds: Formed when one atom donates an electron (becomes cation) and another accepts it (becomes anion); electrostatic attraction between oppositely charged ions.
Significance: Relatively strong in solid state, formed mostly in inorganic molecules like sodium chloride.
3. Hydrogen Bond: Weak attraction between a hydrogen atom and an electronegative atom (oxygen or nitrogen).
Significance: Maintains structure of proteins/nucleic acids, involved in DNA replication.
4. Hydrophobic Interactions: Occur between nonpolar molecules in aqueous environments — nonpolar molecules cluster to minimize water contact.
Significance: Crucial for protein folding and lipid bilayer formation.
5. Hydrophilic Interactions: Occur between polar molecules and water.
Significance: Essential for dissolution of polar/ionic compounds, nutrient transport.
Condensation: All biomolecules join their monomers by condensation/dehydration. An -OH group is removed from one monomer and a -H atom from another. Also called dehydration synthesis since removal of OH and H means removal of a water molecule.
Hydrolysis: A macromolecule (polymer) is broken into smaller fragments by addition of water — the reverse of dehydration synthesis. OH group from water joins one monomer, H joins the second.
★ This breakdown is essential in digestion and cellular respiration. Example: breakdown of maltose into two glucose monomers by addition of water.
Water (H₂O) is "the medium of life" — about two-thirds of our bodies are water, ranging 65-89% across organisms.
| Property | Bonding | Benefit to life |
|---|---|---|
| Best Solvent | Polarity | Provides medium for chemical reactions |
| Maximum heat capacity (4.184 J) | Hydrogen bonding | Keeps temperature constant internally/externally |
| Maximum density at 4°C | Change in hydrogen bonding | Ice floats on water |
| High heat of vaporization (574 kcal/kg) | Hydrogen bonding | Moderates Earth's temperature; cooling via sweat/transpiration |
| Ionization (H⁺, OH⁻ at 10⁻⁷ M) | Covalent bond breaks | Determines acidity/alkalinity of medium |
| Cohesion | Polarity, Hydrogen bonding | Water/nutrients transported roots→leaves; surface tension (water striders) |
1. Solvent properties: due to polarity + hydrogen bonding — charged/polar molecules dissolve, providing a medium for metabolism.
2. Hydrophobic exclusion: non-polar molecules (e.g. lipids) are insoluble, excluded from water, forming membranes.
3. Heat capacity: water absorbs/releases heat with minimal own-temperature change (heat breaks H-bonds) — acts as temperature stabilizer.
4. Heat of vaporization: 574 Kcal/kg — moderates Earth's temperature; cooling effect via transpiration/perspiration.
5. Cohesion: H-bonds let water molecules "stick together" — enables transport in xylem against gravity; gives high surface tension (water strider walks on water).
6. Ionization: water ionizes reversibly to H⁺ and OH⁻ (1 in 550 million molecules at 25°C) — these ions determine pH, affecting enzyme activity.
7. Density: maximum at 4°C; ice (0°C) is less dense than liquid water (H-bonds keep molecules further apart) — ice floats, insulating water below and protecting aquatic life.
Carbohydrates are naturally occurring organic compounds ("hydrated carbon"), synthesized as primary products of photosynthesis in a C:H:O molar ratio of 1:2:1. Empirical formula: C(H₂O)n.
Classification: 1. Monosaccharides 2. Disaccharides 3. Polysaccharides.
Monosaccharides (simple sugars) are single sugar molecules, easily soluble in water, with 3-7 carbon atoms. Pentoses and hexoses are most common; hexoses play a central role in energy storage — glucose (7 energy-storing C-H bonds) is the primary energy-storage molecule.
| Type | C atoms | Formula | Examples |
|---|---|---|---|
| Trioses | 3 | C₃H₆O₃ | Glyceraldehyde, Dihydroxyacetone |
| Tetroses | 4 | C₄H₈O₄ | Erythrose, Erythrulose |
| Pentoses | 5 | C₅H₁₀O₅ | Ribose, Deoxyribose, Ribulose |
| Hexoses | 6 | C₆H₁₂O₆ | Glucose, Fructose, Galactose |
| Heptoses | 7 | C₇H₁₄O₇ | Rare in nature |
Isomers: Molecules with the same molecular formula but different arrangement of atoms (different structural formula). Glucose, fructose, and galactose all share C₆H₁₂O₆.
Fructose — the double-bonded oxygen is on an internal carbon (C2) rather than terminal — glucose and fructose are structural isomers.
Galactose — differs from glucose only in orientation of the OH group at C4 — glucose and galactose are stereoisomers.
When in solution, most monosaccharides form ring structures via an oxygen-bridge between two carbons of the same molecule:
Two forms of D-glucose differ only in the direction of the OH group on carbon 1. α-D-glucose: OH on lower side — polymerizes to starch. β-D-glucose: OH on upper side — polymerizes to cellulose.
Disaccharides are made from two monosaccharides by dehydration synthesis; the covalent bond formed is called a glycosidic bond. On hydrolysis, they yield their monomers. Less soluble than monosaccharides. All have formula C₁₂H₂₂O₁₁.
1. Maltose (Malt Sugar): two glucose monomers, 1,4-glycosidic bond. Found in cereals; intermediate in starch digestion.
2. Lactose (Milk Sugar): galactose 1-4 glucose. Found only in mammalian milk — main energy source for infant mammals.
3. Sucrose (Table Sugar): glucose 1-2 fructose. Most familiar disaccharide, acts as sweetener. Found in phloem vessels — the "transport disaccharide" conducting glucose between plant parts.
Polysaccharides are the most complex and abundant carbohydrates — long chains of monosaccharides joined by glycosidic bonds.
1. Starch — plant storage polysaccharide; insoluble (forms granules, doesn't change water potential). Mixture of amylose (straight, 1,4-linkages, coils into helix) and amylopectin (1,4-linkages + 1,6-branches — more ends, broken down faster by amylase).
2. Glycogen — similar to amylopectin (1,4 + 1,6 linkages); animal storage polysaccharide in muscles/liver; highly branched, broken down very quickly.
3. Cellulose — main component of plant cell walls; glucose monomers (1,4-linkages) but with beta-glucose (alternating inverted) — forms straight chains, not helices. Chains linked by hydrogen bonds into microfibrils → cellulose fibrils (strong/rigid). ★ Amylase cannot break the beta-bond; requires cellulase (found in some bacteria/protozoans — herbivores like cows/termites host these in gut flora). Humans can't digest cellulose (dietary fibre).
4. Chitin — modified cellulose; glucose monomers with a nitrogen-containing group added. Found in exoskeletons of crabs/lobsters/insects and fungal cell walls.
5. Pectin and Lignin — building materials in plant cell walls. 6. Agar — found in red algae cell walls; used as a thickener and lab culture medium. 7. Murein — sugar-peptide polymer in prokaryotic cell walls.
Proteins are polymers formed by inter-linkage of amino acid monomers — the most abundant organic compounds in cells; may have a few to 3000 amino acids (Insulin: 51, Haemoglobin: 574).
An amino acid has four groups attached to the same (alpha) carbon: amino group (NH₂), carboxyl group (COOH), hydrogen (H), and a side group (R).
Occurrence: ~170 types occur in nature; ~25 may be building units of proteins; most proteins are made of 20 types. R group determines each amino acid's identity.
Essential (9): methionine, valine, tryptophan, isoleucine, leucine, lysine, threonine, phenylalanine, histidine.
Non-essential (11): alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, tyrosine.
A covalent bond linking two amino acids is a peptide bond. When two amino acids come together, dehydration synthesis occurs between the amino group of one and carboxyl group of the other, releasing water and forming the peptide bond (N-C).
Polypeptide chain: A dipeptide has an amino group at one end and carboxyl at the other — both ends reactive for further peptide bonds, leading to polypeptide chains. Insulin has 2 polypeptide chains; haemoglobin has 4.
1. Primary Structure — linear arrangement of amino acids; represents number and sequence in a polypeptide chain. All proteins have specific primary structures determined by DNA nucleotide order. ★ Over 10,000 proteins in the human body, each with a specific primary structure. Bonds: peptide bonds (single chain) or disulphide bonds (multiple chains, e.g. insulin's alpha chain 21 aa + beta chain 30 aa).
Substitution example: Sickle cell haemoglobin — valine replaces glutamic acid at position 6 of each beta chain → abnormal sickle-shaped RBCs unable to transport sufficient oxygen (sickle cell anaemia).
2. Secondary Structure — folding/coiling within a polypeptide chain. Coiling → alpha helix; folding → pleated sheet. Maintained by hydrogen bonds between amino/carboxyl groups of nearby amino acids.
3. Tertiary Structure — secondary structure further folds into a complicated globular shape. Maintained by ionic, hydrogen and disulphide bonds. Most stable form: hydrophobic (non-polar) amino acids bury inside, hydrophilic (polar) amino acids face the water surface.
4. Quaternary Structure — aggregation of two or more tertiary polypeptide structures, held by hydrophobic interactions, hydrogen bonds and ionic bonds — the most complex proteins (e.g. haemoglobin's four chains).
| Characteristic | Fibrous Proteins | Globular Proteins |
|---|---|---|
| Shape | Fibrils | Spherical/ellipsoidal |
| Structure | Primary or Secondary | Tertiary or Quaternary |
| Role | Structural | Functional |
| Crystallization | Non-crystalline, elastic | Can be crystallized |
| Solubility | Insoluble | Soluble in salt/acid/base/aqueous alcohol |
| Disorganization | Do not disorganize easily | Disorganized with environmental changes |
| Examples | Silk fibre, Actin, Fibrin, Keratin, Collagen | Enzymes, Antibodies, Hormones, Haemoglobin |
Lipids are a loosely defined group of non-polar molecules, insoluble in water but soluble in organic solvents. Classified as acylglycerols, waxes, phospholipids, terpenes, steroids and prostaglandins.
Composed of glycerol (3C alcohol) + fatty acids. Liquid at room temp = oils (mostly plants, e.g. peanut/corn/castor oil); solid = fats (mostly animals, e.g. butter). Chemically, esters of fatty acids and alcohol, formed by dehydration synthesis. Most widely found: triacylglycerol (triglycerides/neutral lipids) — 3 fatty acids on one glycerol backbone.
Saturated fatty acids: no double bonds, straight chains, high melting point.
Unsaturated fatty acids: double bonds (max 6), bent chains, low melting point. Mono-unsaturated (1 double bond) vs poly-unsaturated (>1).
Animal fats > energy than plant oils (more saturated fatty acids = more C-H bonds).
Derived from acylglycerols; high melting points (solid at room temp). Mixtures of long-chain alkanes (odd-numbered C25-C35), alcohols, ketones, and long-chain fatty acids — no well-defined structure. Chemically inert, strongly hydrophobic — protective coverings on fruits/leaves/skin. Used to waterproof paper, wax polishes, candles, crayons. Honeybees use wax for hexagonal comb chambers; in humans, secreted by outer ear canal glands.
Derivatives of phosphatidic acid (1 glycerol + 2 fatty acids + 1 phosphoric acid), with a nitrogenous base (choline, ethanolamine, or serine) attached. Common example: phosphatidyl-choline (lecithin).
Components: Head = polar (nitrogenous base + phosphate); Tail = non-polar (2 fatty acids). Phosphatidyl-choline forms the lipid bilayer of plasma membranes.
Large, diverse group made of isoprene units (CH₂=C(CH₃)-CH=CH₂ — a branched unsaturated hydrocarbon). Form biologically important pigments — chlorophyll (plants), retinal pigments (eyes). Vitamin A and rubber are also terpenes.
Steroids: carbon skeleton bent into four fused rings (three 6-cornered + one 5-cornered). Cholesterol is a common steroid in animal cell membranes, used to make other steroids (sex hormones). ★ Anabolic steroids (banned today) can cause deep depression, liver damage, etc.
Prostaglandins: modified fatty acids, non-polar tails attached to a 5-carbon ring. Occur in vertebrate tissues as local chemical messengers — stimulate/relax smooth muscles, constrict/expand blood vessels, involved in inflammatory response. Aspirin inhibits prostaglandins.
Sources of energy: most energy-rich nutrient — 1g lipid = 9.5 kcal (vs protein 5.6 kcal, carbohydrate 4.1 kcal). Components of membranes. Biological carriers for fat-soluble vitamins A, D, E, K. Source of fatty acids for metabolism. Mechanical cushion for organs. Insulation beneath skin. Steroids (cholesterol) maintain membranes, aid lipid transport, and are precursors of vitamin D, bile acids, and steroid hormones.
Nucleic acids are polymers of nucleotide units — DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA is found mainly in chromosomes (small amounts in mitochondria/chloroplasts); RNA in nucleolus, ribosomes and cytosol.
A nucleotide = nucleoside + phosphoric acid. A nucleoside = nitrogen base + pentose sugar.
a. Pentose sugars: RNA contains ribose (C₅H₁₀O₅); DNA contains deoxyribose (C₅H₁₀O₄).
b. Nitrogenous bases: Pyrimidines (single-ringed) — cytosine (both), thymine (DNA only), uracil (RNA only). Purines (double-ringed) — adenine and guanine (both DNA & RNA). One base attaches to C1 of pentose sugar → nucleoside.
c. Phosphoric acid: develops an ester linkage with C-5 of the pentose sugar to form a nucleotide. The backbone of nucleic acids is made of sugars and phosphates.
In one nucleotide, phosphoric acid has an ester linkage at C-5 of the pentose sugar. This phosphoric acid develops another ester linkage at C-3 of the pentose sugar of another nucleotide — each phosphoric acid has two ester linkages (one at C-5, one at C-3), together called a phosphodiester linkage, joining two nucleotides.
Ribonucleotides = nucleotides of RNA. Deoxyribonucleotides = nucleotides of DNA (named after their nitrogenous base).
ATP — a triphosphate nucleotide of adenine; three phosphate groups attached to ribose sugar; the "energy currency" of the cell (detaches phosphates → ADP → AMP).
NAD (Nicotinamide Adenine Dinucleotide) — a co-enzyme acting as a hydrogen acceptor in oxidation-reduction reactions.
James D. Watson and Francis Crick, in 1953, put forward the model of DNA:
Two strands held by weak hydrogen bonds — Adenine pairs with Thymine (2 H-bonds), Guanine pairs with Cytosine (3 H-bonds). The two strands run anti-parallel (not the same direction with respect to phosphodiester linkages).
DNA — Location: inside nucleus (eukaryotes) or cytoplasm (prokaryotes, no nucleus); as core molecule in viruses, covered by protein coat.
Function: hereditary material for all organisms (except some viruses); contains the "program" (genes) directing all cellular activities. A gene is a sequence of DNA nucleotides coding for a polypeptide. When a gene is "ON", it's transcribed into RNA then translated into proteins. ★ In E. coli, each DNA strand has ~5 million bases in circular order.
Composed of ribonucleotides, synthesized by joining ribonucleotides against DNA template by transcription.
1. mRNA (Messenger RNA): single strand, sequence complementary to a DNA strand; ~3-4% of total RNA; carries genetic message to ribosomes.
2. tRNA (Transfer RNA): small, helical, clover-leaf shape; ~10-15% of total RNA; transports amino acids to ribosome/mRNA.
3. rRNA (Ribosomal RNA): synthesized in nucleoli, joins ribosomal protein to form ribosomes; ~80% of total RNA; the machinery for protein synthesis.
All organisms use the same basic mechanism of reading and expressing genes — the central dogma.
Transcription: first step — transfer of information from DNA to RNA (RNA copy of gene produced). In prokaryotes occurs in the cytoplasm; in eukaryotes in the nucleus. Requires a promotor sequence to start.
Translation: second step — transfer of information from RNA to proteins (RNA directs protein synthesis). In prokaryotes starts directly in cytoplasm; in eukaryotes mRNA must be transported to cytoplasm. Starts from a start codon coding for Methionine.
Conjugated molecules are formed by the combination of two or more molecules belonging to different categories.
(i) Glycoproteins: covalent linkage between a protein and a carbohydrate polymer. Occur widely as structural components of membranes, blood serum, cellular secretions, cartilage, eyes, skin.
(ii) Glycolipids: covalent linkage between a lipid and a carbohydrate. Integral structural component of membranes.
(iii) Lipoproteins: formed by hydrophobic interactions (not covalent/ionic) between lipids and proteins. Basic structural framework of all plasma membranes; lipids transported in blood as very low-density lipoproteins.
(iv) Nucleoproteins: formed by ionic bonds between chromosomal DNA and proteins e.g. histone proteins bound to DNA form nucleosomes — stabilize chromosomal structure and regulate gene expression.
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