1: Chemical bonds in biology

Section 1: Chemical Bonds in Biology

Chemical bonds are the fundamental forces holding atoms together to form molecules and dictating the structure, stability, and function of all biological macromolecules. Understanding their types, strengths, and properties is essential for grasping biomolecular interactions.

1. Covalent Bonds:

   • Nature: The strongest bonds in biology, formed by the sharing of electron pairs between atoms. They require significant energy to break.
   • Types: Nonpolar covalent bonds involve equal sharing of electrons (e.g., C-C, C-H bonds in hydrocarbon chains of lipids). Polar covalent bonds involve unequal sharing due to differing electronegativities, creating partial charges ($\delta^+$, $\delta^-$) (e.g., O-H, N-H, C-O bonds). This polarity is crucial for hydrogen bonding and solubility.
   • Role: Form the stable backbone of biomolecules (e.g., C-C chains in lipids/sugars, peptide bonds linking amino acids in proteins, phosphodiester bonds in nucleic acid backbones). Define the primary structure.

2. Ionic Bonds (Electrostatic Interactions):

   • Nature: Attraction between fully charged ions (cations +, anions -) resulting from electron transfer. Stronger in nonpolar environments or when shielded less by water.
   • Role: Stabilize protein tertiary/quaternary structure (e.g., salt bridges between acidic (-COO⁻) and basic (-NH₃⁺) amino acid side chains like Asp and Lys). Important in enzyme active sites and protein-DNA interactions.

3. Hydrogen Bonds:

   • Nature: A weak electrostatic attraction (much weaker than covalent) between a hydrogen atom covalently bonded to a highly electronegative atom (O, N, F - the donor) and another electronegative atom (the acceptor). Highly directional.
   • Role: Critical for secondary structure in proteins (e.g., α-helices and β-sheets maintained by backbone N-H⋯O=C bonds). Essential for DNA double helix stability (base pairing: A=T, G$\equiv$C). Mediates water's unique properties and solute-water interactions.

4. Hydrophobic Interactions:

   • Nature: Not a true bond, but a major stabilizing force. Nonpolar molecules or regions (hydrophobic) aggregate in water to minimize disruptive contact with the polar solvent, reducing the ordered water cage (entropy-driven).
   • Role: Primary driver of protein folding (burying hydrophobic residues inside the core) and lipid bilayer formation (hydrophobic tails sequestered away from water). Crucial for membrane integrity and macromolecular assembly.

5. van der Waals Forces:

   • Nature: Very weak, short-range attractions between transient dipoles caused by fluctuating electron clouds in all atoms/molecules (London dispersion forces). Strength increases with molecular surface area contact.
   • Role: Provide stability through cumulative weak interactions in close-packed regions of molecules (e.g., within the hydrophobic core of proteins, between stacked bases in DNA, in substrate binding pockets of enzymes).

6. Disulfide Bonds:

   • Nature: Strong covalent bonds (-S-S-) formed by the oxidation of two cysteine thiol (-SH) groups.
   • Role: Primarily stabilize the tertiary and quaternary structure of extracellular proteins (e.g., antibodies, insulin), locking folds and linking polypeptide chains. Easily reduced to break.