Biochemistry

• Chemical bond is the force of attraction between two atoms, formed to achieve a more stable outer electronic configuration, following the doublet or octet rule
• Types of bonds include:

  • Ionic or electrovalent bond
  • Covalent bond
  • Coordinate bond or dative covalent bond
• Ionic or electrovalent bond is formed by the complete transfer of electrons between atoms in a compound, leading to the electrostatic attraction between oppositely charged ions
• Factors affecting ionic bond formation include low ionization energy, high electron affinity, lattice energy, and electronegativity difference
• Ionic bond formation is favored when the electronegativity difference is very high, leading to the formation of ionic compounds
• Covalent bonds are formed by the sharing of electrons between atoms in a compound, with two main types:

  • Sigma bond (σ)
  • Pi bond (π)
• Sigma bond (σ) occurs with an end-to-end or head-on overlap of atomic orbitals along their inter-nuclear lines
• Pi bond (π) involves a side-to-side or lateral overlap of atomic orbitals away from the inter-nuclear axis of the atoms, being weaker and more reactive than sigma bonds
• Hybridization is the mixing of atomic orbitals of different shapes and energies to form orbitals of equal energy, shape, and direction
• Types of hybridization include:

  • sp hybridization
  • sp2 hybridization
  • sp3 hybridization
  • sp3d Hybridization
  • sp3d2 Hybridization
• Examples of hybridization:

  • Sp3 hybridization (methane: CH4)
  • Sp2 hybridization (ethene: C2H4)
  • Sp hybridization (ethyne: C2H2)
• Coordinate covalent bonds involve shared electron pairs donated by one of the bonded atoms, seen in important organic molecules like haemoglobin
• Three types of chemical bonds:

  • Nonpolar covalent bond: electrons shared equally between atoms
  • Polar covalent bond: electrons shared unequally, resulting in partial charges
  • Ionic bond: one atom transfers electrons to another, forming oppositely charged ions

  
• In compound formation, atoms transfer or share electrons to attain a noble gas configuration
• Formation of multiple bonds:

  • Double bond: one sigma and one pi bond
  • Triple bond: one sigma and two pi bonds
• Octet Rule:

  • Double bond corresponds to sp2 hybridization
  • Triple bond corresponds to sp hybridization
  • Expanded octet: e.g., PCl5 with more than 8 electrons in the valence shell
  • Deficient octet: e.g., BF3
• Valence shell electron pair repulsion (VSEPR) theory:

  • Arrangement of electron pairs minimizes repulsion for stability
  • Lone pair: lone pair repulsion > lone pair: bonded pair repulsion > bonded pair: bonded pair repulsion
• Bond angles:

  • Methane (CH4) with sp3 hybridization has a bond angle of 109°
  • Ethene (C2H4) with sp2 hybridization has a bond angle of 120°
  • Ethyne (C2H2) with sp hybridization has a bond angle of 180°
• Shapes of molecules:

  • Molecule shape affects behavior, e.g., odor, reactivity, taste, drug action
  • Enzyme-substrate interaction follows the "lock and key" hypothesis
• Factors determining polarity of a molecule:

  • Electronegativity difference
  • Shape of the molecule
• Intermolecular forces:

  • Van der Waals forces: predominant in nonpolar molecules
  • Hydrogen bonding: unique permanent dipole-dipole attraction between hydrogen and {N, O, F}
• Hydrogen bonding is possible in HF, slightly possible in HCl, non-existent in HBr and HI

  
• Strong hydrogen bonding in HF results in the associated nature of the molecules, accounting for liquid nature
• Water behaves differently from other hydrides: H2O is liquid due to hydrogen bonding, while H2S, H2Se, and H2Te are gases
• Ionic compounds dissolve in polar solvents but not in non-polar solvents: NaCl dissolves in water but not in ether
• For a solute to dissolve in a solvent, the attraction between the solute particles and the solvent should be greater than the attraction between the solute particles
• Candle wax does not dissolve in water due to strong hydrogen bonding, but dissolves in petrol
• Water's high boiling point ensures it remains a liquid under normal conditions
• Water has a high heat capacity, preventing rapid temperature changes and moderating climate changes
• Water's high heat of vaporization enables it to absorb and store heat, aiding in cooling effects
• Water has an unusual density, with maximum density at 4°C due to hydrogen bonding
• Hydrogen bonding is responsible for the viscosity of liquids, with water being more viscous than benzene
• Liquid surface tension is produced by hydrogen bonding, causing the 'skin effect' on the surface of liquids
• Hydrogen bonding plays a role in determining the molecular conformation of proteins and nucleic acids
• Isomerism is a condition where compounds of the same molecular formula can be represented by different structures
• Structural isomers differ in the way the constituent atoms are connected
• Chain isomerism differs in the chain type, like butane and 2-methylpropane
• Positional isomerism differs in the placement of the functional group, like propanol
• Functional isomerism differs in the functional group, like dimethyl ether and ethanol
• Attachment is a strong reciprocal emotional bond between an infant and a primary caregiver