Biomolecules

Story: Take living tissue like spinach leaves, grind in mortar pestle with trichloroacetic acid Cl3CCOOH like you make chutney with water. Make slurry. Strain through muslin cloth filter. You get two parts: Acid soluble filtrate that passes through = micromolecules small 18-800 Da like glucose, amino acids, fatty acids, nucleotides small soluble. Acid insoluble retentate that stays on filter = macromolecules big >1000 Da like proteins, nucleic acids, polysaccharides plus lipids (lipids are micromolecules but form micelles big so stay in retentate exception).

Now burn the tissue fully. Organic compounds burn into CO2 water gases fly away. Left ash inorganic like Na+ K+ Ca2+ Mg2+ chloride phosphate.

Biomolecules = all carbon compounds in living tissue except minerals. Average composition cell: Water 70-90% most abundant like you are mostly water, Proteins 10-15% next, Carbohydrates, Lipids, Nucleic acids. Once you imagine chutney filter, you never forget analysis.

Primary metabolites directly involved in growth development essential found in all plants universal like daily dal chawal. Examples sugars, amino acids, fatty acids, nucleic acids, chlorophyll. You need them to live.

Secondary metabolites not directly needed for growth but important ecologically for defence attraction like spices drugs toxins. Not found in all plants, stored in vacuole. Classes: Alkaloids morphine codeine from opium, Terpenoids menthol essential oils, Toxins Abrin from Abrus highly toxic one molecule kills, Ricin from castor, Flavonoids anthocyanin colour, Rubber latex, Gums, Spices curcumin turmeric yellow, Drugs Vinblastine Vincristine anticancer from Vinca. Humans use secondary metabolites as drugs spices. Plants make them to protect from herbivores. Remember: Primary = universal daily food, Secondary = special spices drugs toxins not universal but useful for us.

Amino acid general structure: Central alpha carbon with H, Amino NH2, Carboxyl COOH, R variable group that decides type. Simplest Glycine R=H only H. 20 types based on R: Nonpolar aliphatic, Aromatic with benzene ring tryptophan tyrosine phenylalanine (absorb UV), Polar uncharged, Acidic negative glutamic aspartic like sour, Basic positive lysine arginine histidine like basic.

Essential 8 cannot be made by body must take diet like you must buy from market, Non-essential made by body like you make at home. Trick to remember essential: PVT TIM HALL (Phe Val Thr Trp Ile Met His Arg Leu Lys).

Zwitter ion: In neutral pH amino exists as NH3+ and COO- both charges like dual personality acid and base amphoteric.

Proteins polymer of amino acids peptide bond CO-NH formed by dehydration water removed. Levels: Primary sequence of amino acids N to C order like letters in word. Secondary alpha helix right handed 3.6 residues per turn H bonds within chain C=O to N-H like spring coiled keratin hair, Beta pleated sheet parallel antiparallel H bonds between chains like folded paper silk fibroin strong. Tertiary 3D folding due to interactions hydrophobic inside hydrophilic outside disulphide S-S bonds ionic H bonds gives functional shape like origami final shape. Quaternary multiple polypeptides subunits like hemoglobin 2 alpha 2 beta 4 subunits with heme iron carries oxygen. Function transport enzyme hormone structure.

Polysaccharides homopolysaccharides same monosaccharide: Starch alpha glucose storage plants potato you eat daily. Two forms amylose helical unbranched iodine gives blue colour like spring, amylopectin branched iodine red. Glycogen animal storage highly branched tree like highly branched in liver muscle you store energy after eating. Cellulose beta 1-4 straight fibers H bonds between chains structural like rope strong makes paper cotton you cannot digest but cow can. Chitin N-acetyl glucosamine NAG fungal wall insect exoskeleton cockroach, second most abundant after cellulose. Glycosidic bond formed by dehydration.

Lipids fatty acids R-COOH long chain: Saturated palmitic 16C no double bond straight solid like ghee solid, Unsaturated oleic 18:1 one double bond kink bend liquid like oil liquid, Polyunsaturated arachidonic 20:4 four double bonds more kink. More kinks more liquid. Glycerol trihydroxy propane CH2OH-CHOH-CH2OH + 3 fatty acids ester bond makes triglyceride fat oil like you attach three tails to body. Phospholipids lecithin phosphate + choline hydrophilic head water loving hydrophobic tails water fearing bilayer in membrane like head outside tail inside sandwich. Cholesterol 4 fused rings steroid makes hormones vitamin D. Functions energy insulation membrane.

DNA Watson Crick 1953 double helix right handed 20A diameter 34A pitch one turn 10 base pairs antiparallel one strand 5' to 3' other 3' to 5' like two roads opposite direction. Sugar deoxyribose phosphate backbone like side rails of ladder, bases rungs purine double ring A G large, pyrimidine single ring C T small. Chargaff rule A=T 2 H bonds two ropes G=C 3 H bonds three ropes stronger. So AT rich DNA melts easily.

Nucleoside base+sugar like base + sugar without phosphate, Nucleotide base+sugar+phosphate phosphodiester bond linking.

RNA single strand ribose sugar OH extra U instead of T uracil. Types: mRNA messenger codon carries code from DNA to ribosome like message, rRNA ribosomal makes ribosome factory, tRNA transfer clover leaf 76 nucleotides anticodon loop reads codon D loop T psi C loop variable loop CCA 3' end amino acid attachment like adaptor. tRNA shape like clover or L-shape. Functions: DNA stores genetic information, RNA helps in protein synthesis. Even dumb person remembers A=T 2 ropes G=C 3 ropes stronger.

Structure: Active site cleft where substrate binds like key hole. Enzyme substrate complex ES -> Enzyme product EP -> E + P free enzyme again. Like worker holds material works and leaves.

Models: Lock and key Emil Fischer 1894 rigid lock and key fixed shape like exact lock key. Induced fit Daniel Koshland 1958 flexible active site changes shape to fit substrate like hand in glove hand adjusts.

Properties: Highly specific one enzyme one substrate, Accelerates, Not consumed, Lower activation energy, Affected by temperature pH substrate.

6 classes IUB: Oxidoreductases dehydrogenases oxidation reduction NAD example alcohol dehydrogenase, Transferases transfer groups, Hydrolases hydrolysis water breaking sucrase, Lyases remove groups non-hydrolytic aldolase, Isomerases interconvert isomers, Ligases join bonds using ATP DNA ligase joins DNA like glue.

Factors: Temperature bell curve optimum 37C low slow like cold you slow high denature after 45C like egg boils enzyme dies. pH optimum 6-8 bell curve acid base denature. Substrate concentration hyperbolic Michaelis Menten curve Km at half Vmax Km low means high affinity like low Km means loves substrate.

Cofactors: Non-protein helpers Apoenzyme protein + Cofactor = Holoenzyme active. Prosthetic group tightly bound heme Fe in hemoglobin catalase like fixed part, Coenzyme loosely bound organic NAD NADP CoA FAD transient like visiting helper, Metal ions Zn2+ carbonic anhydrase Fe2+ catalase Mg2+ hexokinase like metal tools.

Inhibition: Competitive inhibitor similar shape competes for active site increases Km reversible like fake key blocks lock example malonate inhibits succinate dehydrogenase similar shape. Non-competitive binds allosteric site other than active changes shape decreases Vmax like lock changed cannot open. Feedback inhibition end product inhibits first enzyme of pathway regulation like final product says stop production.