--- module: 087-01 language: en chapter: 87 title: "Biomolecules, Protein Structure, Enzymes, Cofactors, and Biochemical Regulation" module_title: "Water, chemical bonding, acid–base chemistry, and biological macromolecules" source_sha256: 8c9d2e995136612fce0a593ee206bd8095c729f90dc42951a095c82b33f7d36c --- # Water, bonding, acid-base, and macromolecules ## Chemical foundations ### Organised non-equilibrium systems #### Crowding, compartments, catalysts, energy input ### Covalent bonds share electron pairs #### Geometry and electron distribution set shape ### Carbon: four bonds, chains, rings, stereoisomers ### N, O, P, S add acid-base, redox, transfer ### Functional groups confer recurring properties ## Noncovalent forces ### Electronegativity makes bonds polar #### Water: partial negative O, partial positive H ### Hydrogen bonds: weak singly, strong collectively #### Water, secondary structure, base pairing #### Reversible at physiological temperature ### Ionic interactions depend on water, salt, distance ### Van der Waals forces matter at close fit ### Hydrophobic effect from water and entropy #### Drives membrane formation and folding ## Water and solutions ### Hydration shells and high dielectric constant ### Cohesion, heat capacity, heat of vaporisation #### Temperature stability and evaporative cooling ### Takes part in hydrolysis, condensation, redox ### Moles, molarity, osmotically active particles #### Per litre versus per kilogram of solvent ### Activity governs non-ideal solutions ### Tonicity depends on nonpenetrating solutes #### Urea raises osmolarity, adds little tonicity ## Acids, bases, and buffers ### Strong acids dissociate, weak acids equilibrate ### pKa: pH of equal conjugate pair #### Henderson-Hasselbalch relation ### Buffers work best near pKa ### Bicarbonate links lungs and kidneys ### Phosphate and proteins, especially histidine ### Buffering does not remove acid #### Excretion or metabolism required ### Ionisation changes with pH #### Isoelectric point: zero net charge #### Uncharged forms cross membranes readily ## Redox and energetics ### Oxidation loses, reduction gains electrons ### Reduction potential: tendency to accept ### Energy captured by carriers and gradients ### Negative free energy says nothing about rate #### Enzymes leave equilibrium position unchanged ### Coupling to ATP hydrolysis ## Carbohydrates and lipids ### Monosaccharides cyclise and form anomers ### Glycosidic bond orientation and specificity #### Starch digested, cellulose not efficiently ### Glycogen: highly branched, many ends ### Glycosaminoglycans and glycan recognition #### Blood-group antigens ### Cis double bonds bend chains, raise fluidity ### Triacylglycerols store energy without water ### Amphipathic lipids self-assemble into bilayers ### Cholesterol: fluidity and precursor ## Proteins and nucleic acids ### L amino acids and side-chain classes ### Essential amino acids come from diet ### Peptide bond restricts rotation ### Sequence determines folding and fate ### Nucleotides: base, pentose, phosphate #### Purines fused rings, pyrimidines one ring ### DNA has thymine, RNA usually uracil ### Phosphodiester backbone and directionality ### Pairing gives complementarity, stacking stability ### Diverse RNA roles, nucleotide signals ## Assembly and synthesis ### Noncovalent assembly into complexes #### Ribosomes, membranes, chromatin ### Weak bonds reversible, covalent bonds durable ### Polymers built from activated monomers #### Enzymes control sequence and direction ### Name groups, forces, compartment, energy source