Fundamentals of Chemistry

Fundamentals of Chemistry

• Atoms are the smallest particles with properties of a given element.
• Atoms contain protons, neutrons, and electrons.
• A unified mass unit is 1/12 the mass of a carbon-12 atom.
• Atomic number (Z) is the arrangement of elements in the periodic table.
• Ionization energy is the energy needed to remove a valence electron.
• Electron affinity is the energy change when an electron is added.
• Electronegativity is an atom's ability to attract electrons.
• Atomic radius is the distance from the nucleus to the outermost electron shell.
• Isotopes are variants of an element with different mass numbers (different number of neutrons).
• Carbon has two stable isotopes: carbon-12 and carbon-13.
• Nuclide symbols represent mass number on top and atomic number on bottom.
• Rutherford-Bohr model describes positively charged nuclei surrounded by negatively charged electrons in specific orbits. It is not accurate for atoms with more than one electron.
• Quantum mechanical model describes electrons as having wave-like properties and their behaviour following the Schrödinger wave equation.

Molecular Geometry

• Wave function describes the probability of finding an electron at a particular point in space.
• Atomic orbitals are regions of space with high probability of finding an electron.
• Quantum numbers describe the size, shape, orientation, and properties of electrons(principal/shell/orbital/magnetic/spin)
• Orbitals with the same energy are described as degenerate.
• Aufbau principle: electrons fill the lowest energy orbitals first.
• Hund's rule: electrons fill separate orbitals before pairing up in the same orbital.
• Ionic bond: electron transfer to a more electronegative atom.
• Covalent bond: sharing of electrons (less than one difference in electronegativity).
• Polar covalent bond: Unequal sharing of electrons.
• Structural formula: order of chemical groups.

Valence Bond theory

• Overlap of atomic orbitals forms bonds.
• Sigma bonds form end-to-end overlap.
• Pi bonds form sideways overlap.
• Hybridisation: new set of atomic orbitals.

Molecular Orbital theory

• Molecular orbitals describe regions of space where electrons are likely to be found in molecules.

Moles & molar mass

• Moles: number of discrete particles.
• Avogadro's number is 6.022 × 10^23
• Molar mass: mass of one mole of a substance.
• Number of moles = mass/molar mass

Acids and bases

• Water dissociates into H₃O⁺ and OH⁻.

• Rate of disassociation = K₁ [AB]

• Rate of association = K₂ [A][B]

• At equilibrium, K₁[AB] = K₂ [A][B].

• The dissociation constant (K) can be calculated.

• lonic product of water Kw = [H⁺][OH⁻] = 1 X 10⁻¹⁴ M².

Biomolecular Bonding

• Intermolecular forces: forces between molecules.
• Dipoles: charge distributed across the molecule. Can cause polarity.
• Permanent dipole interactions: non-symmetric distribution of charge.
• London Dispersion forces: transient dipoles lead to attraction within/between molecules. Larger molecules mean stronger LDFs
• Hydrogen Bonds: very electronegative atoms attract electron-deficient hydrogen.
• Ionic bonds: electrostatic forces between oppositely charged groups.
• Melting Points: Higher melting points result in better packing in solids and more symmetry.

Thermodynamic

• Thermodynamics: the relative energies between reactants and products.
• System: reactants and products.
• Surroundings: everything else outside the system.
• Boundary: where the two meet.
• Total energy in an isolated system doesn’t change.
• Total energy of system and surrounding won’t change.
• Heat: energy per mole.
• Enthalpy: total energy a chemical system possesses.
• Kinetic energy: energy in the form of moving electrons, vibration of atoms, rotation/translation of molecules.
• Chemical potential energy: covalent/ionic bonds.

Enzymes and Enzyme Kinetics

• Enzymes catalyse biochemical reactions by lowering the energy required to reach the transition state.
• Substrate binds to the active site forming an enzyme-substrate complex.
• Enzyme-substrate complex undergoes a reaction then releases the product forming free enzyme. This interaction between the substrate and functional groups lowers the activation energy.
• Reaction velocity v maximum at high substrate concentration. At low concentration of substrate reaction rate is directly proportional to substrate concentration.
• Reaction velocity v is the maximum reaction rate when the enzyme is saturated, unaffected by changes in substrate concentration.
• Reaction velocity depends on substrate concentration ([S], first order kinetics) at low concentrations, and maximum reaction velocity (Vmax) at high substrate concentrations(zero order kinetics).
• Michaelis-Menten equation V = (Vmax[S])/(Km+[S])
• Lineweaver-Burk plot can be used to determine K_m(Michaelis constant).
• KM is the substrate concentration at half of Vmax.
• kcat (turnover number of the enzyme) = k2, max number of chemical conversions per second the enzyme will make.

Allosteric Effects and Regulation of Enzymes

• Multi-subunit proteins respond to small changes in the substrate concentration.
• Substrate binding at active site causes a change to the enzymes quaternary structure, affecting the reaction rate.
• Allosteric binding of substrate can either inhibit or activate enzymes.
• Inhibitors: molecules that reduce enzyme activity by binding allosteric sites and reducing active site activity.
• Effectors/activators: molecules that cause conformational changes and increase the active site’s efficiency.

Glycolysis and Gluconeogenesis

• Glycolysis: glucose to pyruvate; occurs in cytoplasm; 10 steps using enzymes
• Gluconeogenesis: pyruvate to glucose; occurs in cytoplasm and mitochondria; takes place as it is the reversal of glycolysis.

Oxidative Phosphorylation

• Pyruvate is converted to acetyl-CoA, reducing NAD+ to NADH and releasing CO₂ using pyruvate dehydrogenase complex.
• Acetyl-CoA enters the citric acid cycle (TCA/Krebs).
• Oxidation of Acetyl-CoA in the citric acid cycle removes CO₂ and reduces electron carriers.
• Electron carriers (e.g., NADH, FADH₂) pass electrons to the electron transport chain (ETC), generating a proton gradient.
• This gradient is used to drive ATP synthesis through ATP synthase.

Other biochemical concepts

• Protein purification: various methods used to isolate proteins.
• Lipid aggregation: hydrophobic/hydrophilic properties of lipids drive the formation of micelles and bilayer membranes.
• Nucleic acids: linear polymers of nucleotides containing coded information.
• Monomeric nucleotides: molecules with functions like energy.
• Amino acids: building blocks of proteins with central α–carbon atom connected to an amino group, carboxylic acid and side chain.
• Proteins: long chains of amino acids.