Biomolecules

🎯 Key Points

• Protein structure levels: primary (sequence) → secondary (helix/sheet) → tertiary (3D fold) → quaternary (multiple subunits)
• Enzymes lower activation energy, don't change reaction equilibrium; Km = substrate concentration at half Vmax (lower Km = higher affinity)
• Competitive inhibition: overcome by MORE substrate (inhibitor competes at active site); Non-competitive: NOT overcome by more substrate (binds elsewhere, changes shape)
• DNA: A-T (2 H-bonds), G-C (3 H-bonds) — G-C rich DNA is more thermally stable; RNA uses U instead of T and is single-stranded
• Saturated fats (no double bonds) are solid at room temp; unsaturated fats (have double bonds) are liquid
• Coenzymes (NAD⁺, FAD, vitamin-derived) bind transiently; prosthetic groups bind permanently; metal ion cofactors form coordination bonds at the active site

Carbohydrates

• Monosaccharides: glucose, fructose, galactose (C6H12O6)
• Disaccharides: sucrose (glucose+fructose), lactose, maltose; glycosidic bond
• Polysaccharides: starch (storage in plants), glycogen (storage in animals), cellulose (structural in plants), chitin (fungal cell wall, insect exoskeleton)

Proteins

• Made of amino acids linked by peptide bonds
• 20 standard amino acids; 8 are essential (from diet)
• Levels of structure: primary (amino acid sequence), secondary (alpha helix, beta sheet), tertiary (3D folding), quaternary (multiple subunits)
• Functions: enzymes, hormones (insulin), antibodies, structural (collagen, keratin), transport (haemoglobin)

Lipids

• Triglycerides (fats/oils): glycerol + 3 fatty acids; energy storage
• Phospholipids: form cell membranes (bilayer)
• Steroids: cholesterol, sex hormones (testosterone, oestrogen), cortisol
• Saturated fats: no double bonds (solid at room temp); unsaturated: one or more double bonds

Nucleic Acids

• DNA: deoxyribose + phosphate + nitrogenous base (A, T, G, C)
• RNA: ribose + phosphate + base (A, U, G, C); single stranded
• Types of RNA: mRNA (messenger), tRNA (transfer), rRNA (ribosomal)

Enzymes

• Biological catalysts (mostly proteins); lower activation energy
• Lock and key model vs induced fit model
• Active site: where substrate binds
• Factors affecting enzyme activity: temperature, pH, substrate concentration, inhibitors
• Michaelis-Menten kinetics: Km (affinity), Vmax
• Inhibitors: competitive (block active site), non-competitive (bind allosteric site)
• Cofactors: inorganic (Zn2+, Fe2+); coenzymes: organic vitamins (NAD+, FAD)

Enzyme Classification by Reaction Type

• Oxidoreductases: catalyse oxidation-reduction between two substrates (e.g. dehydrogenases)
• Transferases: catalyse transfer of a group (other than H) from one substrate to another (e.g. transaminases)
• Hydrolases: catalyse hydrolysis of bonds (ester, glycosidic, peptide) using water (e.g. amylase, lipase)
• Lyases: catalyse removal of groups without hydrolysis, often forming a double bond (e.g. decarboxylases)
• Isomerases: catalyse interconversion of optical, geometric, or positional isomers
• Ligases: catalyse joining of two molecules using ATP energy, forming C-O, C-S, C-N, or C-C bonds (e.g. DNA ligase)

Factors Affecting Enzyme Activity

• Temperature: activity increases with temperature up to an optimum (often around 37 to 40 degrees C in humans), beyond which the enzyme denatures and activity falls sharply
• pH: each enzyme has an optimum pH (pepsin works best around pH 2, trypsin around pH 8); extreme pH denatures the enzyme
• Substrate concentration: rate increases with substrate concentration until all active sites are saturated, after which rate plateaus at Vmax regardless of further substrate increase
• Enzyme concentration: rate generally increases proportionally with enzyme concentration if substrate is not limiting

Enzyme Inhibition

• Competitive inhibition: inhibitor closely resembles the substrate and competes for the active site; effect can be overcome by increasing substrate concentration (e.g. malonate inhibiting succinate dehydrogenase)
• Non-competitive inhibition: inhibitor binds at a site other than the active site (allosteric site), changing enzyme shape so it cannot bind substrate effectively; not overcome by raising substrate concentration
• Feedback inhibition: end product of a metabolic pathway inhibits an enzyme acting early in the pathway, controlling the rate of the whole pathway

Cofactors and Coenzymes

• Many enzymes need additional non-protein components to function, collectively called cofactors
• Prosthetic groups: organic cofactors tightly/permanently bound to the enzyme (e.g. heme in catalase)
• Coenzymes: organic cofactors that associate transiently with the enzyme, often vitamin derivatives (NAD+, NADP+, FAD, coenzyme A)
• Metal ions (inorganic cofactors): form coordination bonds with side chains at the active site and with the substrate (e.g. Zn2+ in carboxypeptidase, Mg2+ in many phosphatases)

How to Analyse the Chemical Composition of Living Tissue

• To find what a tissue is made of, a sample (a vegetable piece, a slice of liver, etc.) is ground in trichloroacetic acid to form a slurry, which is then strained/filtered to yield a filtrate (acid-soluble pool) and a retentate (acid-insoluble pool)
• The acid-soluble fraction contains thousands of small molecules (micromolecules): amino acids, nucleotides, simple sugars, vitamins, and other small metabolites
• The acid-insoluble fraction contains the macromolecules: proteins, nucleic acids, polysaccharides, and lipids
• Analysing tissue for elements versus for compounds gives different pictures; the same handful of elements (C, H, O, N, S, P and a few others) that build living tissue also occur in non-living matter, but their RELATIVE proportions differ, with carbon and hydrogen being relatively more abundant in living organisms

Micromolecules and Biomacromolecules

• Molecules in the acid-soluble pool have molecular weights roughly in the range of 18 to about 800 daltons (Da) and are called micromolecules or simple biomolecules
• Molecules recovered in the acid-insoluble fraction have molecular weights greater than about ten thousand daltons and are called macromolecules or biomacromolecules
• The four classes of biomacromolecules are proteins, nucleic acids, polysaccharides (all polymers, hence true macromolecules) and lipids
• Lipids are an anomaly: their individual molecular weights are not very high (usually under 800 Da), yet they appear in the acid-insoluble (macromolecular) fraction because they assemble into large membrane structures/vesicles that get trapped during filtration; so they are grouped with macromolecules even though they are not strictly true macromolecules
• In the average chemical composition of a cell, water is by far the most abundant (about 70 to 90%), followed by proteins and the other macromolecules; inorganic ions form only a small percentage

Primary and Secondary Metabolites

• Primary metabolites: biomolecules with clearly identifiable functions and direct roles in normal physiology (growth, development, reproduction) — e.g. amino acids, sugars, nucleotides, lipids; these are found in all living cells
• Secondary metabolites: biomolecules found especially in plants, fungi and microbes whose roles in the producer's own metabolism are often not directly understood, yet many are very useful to humans — e.g. alkaloids (morphine, codeine), flavonoids, terpenoids, essential oils, rubber, gums, drugs, pigments (carotenoids, anthocyanins), toxins, lectins and antibiotics
• Several secondary metabolites serve ecological or defensive roles (deterring herbivores, attracting pollinators, chemical defence) even where their metabolic purpose in the producer is unclear

Nature of Bond Linkages in Polysaccharides

• Polysaccharides are long chains of sugar (monosaccharide) units joined by glycosidic bonds, formed between carbon atoms of adjacent sugars with the loss of a water molecule
• A polysaccharide chain such as starch or glycogen has a reducing end and a non-reducing end; conventionally the right end is the reducing end and the left end is the non-reducing end
• Starch forms helical secondary structures whose coils can hold iodine (I₂) molecules, which is why starch gives a blue-black colour with iodine; cellulose does not form such complex helices and therefore does not hold iodine
• Starch (plants) and glycogen (animals) are storage polysaccharides, whereas cellulose is a structural polysaccharide of plant cell walls made solely of glucose units with no complex helices
• Some complex polysaccharides contain modified/amino-sugar units — for example chitin (in fungal walls and arthropod exoskeletons) contains nitrogen-bearing amino-sugars; inulin is a polymer of fructose

Dynamic State of Body Constituents, Metabolism and the Living State

• Metabolism is the sum total of all chemical reactions occurring in the body; every biomolecule is constantly being made and broken down (turned over), so body constituents are in a dynamic state rather than being fixed
• These reactions occur as metabolic pathways in which one metabolite is converted into another through a series of enzyme-catalysed steps; practically no metabolic reaction in the body ever occurs on its own (all are catalysed)
• Metabolic pathways are of two kinds: anabolic (biosynthetic — building complex molecules from simpler ones and consuming energy, e.g. protein synthesis from amino acids) and catabolic (breaking complex molecules down to simpler ones and releasing energy, e.g. breakdown of glucose to lactic acid)
• Metabolic basis for living: the energy released by catabolic pathways is used to drive energy-requiring anabolic processes and to perform biological work, coupling breakdown to biosynthesis
• The living state: living organisms exist in a metabolic, non-equilibrium steady state that lets them perform work — reaching true chemical equilibrium would mean death. Metabolism continuously keeps the system away from equilibrium, so the living state and metabolism are effectively synonymous; without metabolism there is no living state

🚀 NEET Advanced Edge

Reading a Michaelis-Menten / Lineweaver-Burk plot: On a Michaelis-Menten curve (rate vs [S]), competitive inhibition raises the apparent Km (more substrate needed to reach half-Vmax) but Vmax stays the SAME (given enough substrate, full rate is still reachable); non-competitive inhibition LOWERS Vmax while Km stays unchanged (since the enzyme population's intrinsic activity is reduced, not its substrate affinity).

Allosteric / feedback-inhibited pathways: In a multi-step pathway A→B→C→D, if D allosterically inhibits the FIRST enzyme (A→B), this is negative feedback — a classic exam diagram-reading question where you must trace which step is regulated, not assume it's the last one.

Why enzyme activity drops sharply (not gradually) past the optimum temperature: Heat disrupts the weak hydrogen bonds and hydrophobic interactions maintaining tertiary structure, causing denaturation — an irreversible loss of the specific 3D shape needed for substrate binding, which is why the activity-vs-temperature curve falls off a "cliff" rather than declining smoothly.