Introduction
Are all living organisms made of the same chemicals? Elemental analysis of living tissue and of earth's crust gives similar lists of elements, but living organisms have a higher relative abundance of carbon and hydrogen. This chapter shows how chemical composition is analysed, the kinds of biomolecules found, the structure of proteins, polysaccharides and nucleic acids, and the working of enzymes.
Key Concepts
9.1 How to Analyse Chemical Composition?
Grind living tissue in trichloroacetic acid (Cl₃CCOOH) and strain → filtrate = acid-soluble pool and retentate = acid-insoluble fraction. Thousands of organic compounds are in the acid-soluble pool.Carbon compounds from living tissues are called biomolecules.Wet weight → dry weight → ash: burning removes carbon compounds (as CO₂ and water vapour); the ash contains inorganic elements (calcium, magnesium, etc.).Element comparison (% weight, earth's crust vs human body): H 0.14 vs 9.5; C 0.03 vs 18.5; O 46.6 vs 65.0; Si 27.7 vs negligible.Amino acids: amino group and acidic group on the same α-carbon (α-amino acids); substituted methanes with H, carboxyl, amino and a variable R group. Only 20 types occur in proteins – e.g., glycine (R = H), alanine (methyl), serine (hydroxy methyl). Acidic (glutamic acid), basic (lysine), neutral (valine), aromatic (tyrosine, phenylalanine, tryptophan). Ionisable –NH₂ and –COOH give the zwitterionic form.Lipids: generally water insoluble. Fatty acid = carboxyl group + R group (1 to 19 carbons). Palmitic acid 16 C; arachidonic acid 20 C (including carboxyl carbon). Saturated (no double bond) or unsaturated. Glycerol = trihydroxy propane; esterified with fatty acids → mono-, di-, triglycerides (fats and oils by melting point; oils like gingelly oil stay liquid in winter). Phospholipids (e.g., lecithin) occur in cell membranes.Nitrogen bases: adenine, guanine, cytosine, uracil, thymine. Base + sugar = nucleoside (adenosine, guanosine, thymidine, uridine, cytidine); + phosphate = nucleotide (adenylic, guanylic, thymidylic, uridylic, cytidylic acids). DNA and RNA consist of nucleotides.9.2 Primary and Secondary Metabolites
Primary metabolites (amino acids, sugars, etc.) have identifiable functions in normal physiology.Secondary metabolites in plants, fungi and microbes: pigments (carotenoids, anthocyanins), alkaloids (morphine, codeine), terpenoids, essential oils (lemon grass oil), toxins (abrin, ricin), lectins (concanavalin A), drugs (vinblastin, curcumin), polymeric substances (rubber, gums, cellulose). Many are useful to human welfare; some have ecological importance.9.3 Biomacromolecules
Acid-soluble compounds: molecular weights 18 to about 800 Da.Acid-insoluble fraction: only proteins, nucleic acids, polysaccharides and lipids; except lipids, their molecular weights are 10,000 Da and above.Micromolecules (below 1000 Da) vs macromolecules (acid-insoluble).Lipids are not strictly macromolecules – they come in the insoluble fraction because grinding breaks membranes into water-insoluble vesicles.Average cell composition (% of cell mass): water 70–90, proteins 10–15, carbohydrates 3, lipids 2, nucleic acids 5–7, ions 1. Water is the most abundant chemical.9.4 Proteins
Polypeptides – linear chains of amino acids joined by peptide bonds; heteropolymers (20 types of amino acids).Essential amino acids come from diet; non-essential ones are made by the body.Functions (examples): collagen – intercellular ground substance; trypsin – enzyme; insulin – hormone; antibody – fights infection; receptor – sensory reception; GLUT-4 – glucose transport into cells.Collagen is the most abundant protein in the animal world; RuBisCO is the most abundant protein in the whole biosphere.9.5 Polysaccharides
Long chains of sugars. Cellulose – homopolymer of glucose; starch – plant energy store; glycogen – animal variant; inulin – polymer of fructose.In a chain, the right end is the reducing end, the left end the non-reducing end.Starch forms helical secondary structures and holds I₂ → blue colour; cellulose has no complex helices and cannot hold I₂.Plant cell walls, paper and cotton are cellulosic. Complex polysaccharides with amino-sugars (glucosamine, N-acetyl galactosamine); arthropod exoskeleton has chitin.9.6 Nucleic Acids
Polynucleotides; together with polysaccharides and polypeptides, the true macromolecular fraction.Nucleotide = heterocyclic base + monosaccharide + phosphate.Adenine and guanine are substituted purines; uracil, cytosine, thymine are pyrimidines.Sugar: ribose (RNA) or 2′ deoxyribose (DNA).9.7 Structure of Proteins
Primary: sequence of amino acids; first = N-terminal, last = C-terminal.Secondary: parts folded as a helix – only right-handed helices in proteins – and other forms (e.g., β-pleated sheet).Tertiary: chain folded upon itself like a hollow woollen ball; gives the 3-D view; absolutely necessary for biological activity.Quaternary: arrangement of several subunits. Adult human haemoglobin = 4 subunits (2 α + 2 β).9.8 Enzymes
Almost all enzymes are proteins; some nucleic acids act as enzymes – ribozymes.Active site = crevice or pocket where substrate fits.Unlike inorganic catalysts, enzymes get damaged at high temperatures (say above 40°C); enzymes from thermophilic organisms stay active up to 80–90°C.#### 9.8.1 Chemical Reactions
Physical change: no bond breaking (shape or state change). Chemical reaction: bonds broken and formed, e.g., Ba(OH)₂ + H₂SO₄ → BaSO₄ + 2H₂O.Rate = amount of product formed per unit time (δP/δt). Rule of thumb: rate doubles or halves for every 10°C change.Carbonic anhydrase: CO₂ + H₂O → H₂CO₃. Without enzyme about 200 molecules per hour; with enzyme about 600,000 molecules per second – about 10 million times faster.Metabolic pathway: multistep reactions, e.g., glucose → 2 pyruvic acid through ten enzyme-catalysed steps. Anaerobic muscle → lactic acid; yeast fermentation → ethanol.#### 9.8.2 How do Enzymes achieve High Rates?
Substrate (S) binds the active site → obligatory, transient ES complex → transition state structure → product (P).Activation energy = difference between the energy of S and the transition state. Enzymes lower this barrier.If P is at a lower energy than S, the reaction is exothermic.#### 9.8.3 Nature of Enzyme Action
E + S ⇌ ES → EP → E + P.Catalytic cycle: (1) substrate binds active site; (2) binding induces the enzyme to change shape and fit tightly; (3) bonds of substrate broken, EP complex forms; (4) products released, enzyme free for another cycle.#### 9.8.4 Factors Affecting Enzyme Activity
Temperature and pH: each enzyme has an optimum; low temperature keeps enzyme temporarily inactive; high temperature denatures it.Substrate concentration: velocity rises then reaches Vmax, as all enzyme molecules become saturated.Inhibition: a competitive inhibitor resembles the substrate and competes for the active site, e.g., malonate inhibits succinic dehydrogenase (substrate succinate). Used to control bacterial pathogens.#### 9.8.5 Classification (6 classes, each with 4–13 subclasses; four-digit number)
Oxidoreductases/dehydrogenases – oxidoreduction between S and S′.Transferases – transfer a group G (other than hydrogen).Hydrolases – hydrolysis of ester, ether, peptide, glycosidic, C–C, C–halide or P–N bonds.Lyases – remove groups by mechanisms other than hydrolysis, leaving double bonds.Isomerases – inter-convert optical, geometric or positional isomers.Ligases – link two compounds (C–O, C–S, C–N, P–O bonds).#### 9.8.6 Co-factors
Protein part = apoenzyme. Three kinds of cofactors:Prosthetic groups – organic, tightly bound; e.g., haem in peroxidase and catalase.Co-enzymes – organic, transient association; many contain vitamins, e.g., NAD and NADP contain niacin.Metal ions – e.g., zinc for carboxypeptidase.Removing the cofactor destroys catalytic activity.Diagrams to Know
General amino acid structure (α-carbon with H, NH₂, COOH, R) and zwitterion.Levels of protein structure: primary, secondary (α-helix, β-pleated sheet), tertiary, quaternary.Energy profile: substrate, transition state, product, activation energy with and without enzyme.Graphs of enzyme activity vs pH, vs temperature, and velocity vs substrate concentration (Vmax, Km).Key-Facts Sheet
Acid-soluble pool: 18–800 Da; macromolecules ≥ 10,000 Da (except lipids).20 amino acids; 5 nitrogen bases; purines A, G; pyrimidines C, T, U.Water 70–90% of cell mass.Most abundant protein: collagen (animals), RuBisCO (biosphere).Starch–I₂ blue; cellulose cannot hold I₂; inulin = fructose polymer; chitin in arthropods.Haemoglobin: 2α + 2β.Carbonic anhydrase speeds reaction about 10 million times.Exam Focus (from exercises)
What are macromolecules? Give examples (proteins, nucleic acids, polysaccharides).Tertiary structure of proteins; composition of a triglyceride (glycerol esterified with three fatty acids).Draw alanine (R = methyl group).Important properties of enzymes: substrate specificity, optimum temperature and pH, denaturation at high temperature, lowering of activation energy, inhibition.Key Terms
Biomolecule (जैव अणु), Amino acid (अमीनो अम्ल), Protein (प्रोटीन), Polysaccharide (बहुशर्करा), Nucleotide (न्यूक्लियोटाइड), Nucleic acid (न्यूक्लिक अम्ल), Enzyme (एंजाइम / प्रकिण्व), Active site (सक्रिय स्थल), Substrate (क्रियाधार), Activation energy (सक्रियण ऊर्जा), Inhibitor (संदमक), Cofactor (सहकारक), Apoenzyme (एपोएंजाइम), Metabolite (उपापचयज), Peptide bond (पेप्टाइड बंध)Common Mistakes
Calling lipids true macromolecules – they appear in the acid-insoluble fraction only because membranes form insoluble vesicles.Mixing up purines (A, G) and pyrimidines (C, T, U).Saying proteins have left-handed helices – only right-handed helices are found.Confusing prosthetic groups (tightly bound) with co-enzymes (transiently bound).Thinking enzymes raise activation energy – they lower it.