Atoms are the building blocks of life, made up of protons, neutrons, and electrons. These tiny particles form chemical bonds, creating molecules essential for biological processes. Understanding atomic structure is key to grasping how living organisms function at the molecular level.

Chemical bonds come in various forms, each playing a unique role in biology. From strong covalent bonds in organic molecules to weak hydrogen bonds in DNA, these connections shape the structure and function of biomolecules, influencing everything from cell membranes to protein folding.

Atomic Structure and Chemical Bonds

Structure of atoms

• Atoms are the fundamental building blocks of matter composed of subatomic particles
  • Protons are positively charged particles located in the nucleus
  • Neutrons are neutral particles located in the nucleus
  • Electrons are negatively charged particles orbiting the nucleus in shells (energy levels)
    • The outermost electrons are called valence electrons and are crucial for chemical bonding
• Atomic number indicates the number of protons in an atom and determines the element's identity (carbon has 6 protons)
• Mass number represents the sum of protons and neutrons in an atom (carbon-12 has 6 protons and 6 neutrons)
• Isotopes are atoms of the same element with different numbers of neutrons (carbon-12 and carbon-14)

Formation of chemical bonds

• Chemical bonds are attractive forces between atoms that hold them together, allowing atoms to achieve a stable electronic configuration (octet rule)
• Covalent bonds involve the sharing of electrons between atoms
  • Nonpolar covalent bonds have equal sharing of electrons (C-C bond in hydrocarbons)
  • Polar covalent bonds have unequal sharing of electrons due to electronegativity differences (O-H bond in water)
• Ionic bonds are electrostatic attractions between oppositely charged ions formed when electrons are transferred from one atom to another (Na+ and Cl- in sodium chloride)
• Hydrogen bonds are weak electrostatic attractions between a hydrogen atom and a strongly electronegative atom like oxygen or nitrogen (between water molecules)

Types of bonds in biology

• Covalent bonds are strong and stable bonds commonly found in organic molecules like carbohydrates, lipids, proteins, and nucleic acids, providing structural stability
• Ionic bonds are strong electrostatic attractions found in salts and minerals such as sodium chloride and calcium phosphate, important in maintaining proper electrolyte balance in cells and body fluids
• Hydrogen bonds are weaker than covalent and ionic bonds but crucial in maintaining the structure of water and the secondary structure of proteins and nucleic acids, contributing to the specificity of molecular interactions in biological systems like enzyme-substrate binding and DNA base pairing

Molecular Properties

• Electronegativity is the ability of an atom to attract electrons in a chemical bond, influencing bond polarity
• The octet rule states that atoms tend to gain, lose, or share electrons to achieve a stable electron configuration with eight valence electrons
• Molecular geometry refers to the three-dimensional arrangement of atoms in a molecule, affecting its properties
• Polarity in molecules arises from an uneven distribution of charge due to differences in electronegativity and molecular geometry

Molecules in Biological Systems

Types of bonds in biology

• van der Waals forces are weak intermolecular attractions between molecules
  • Dispersion forces are temporary dipoles induced by the movement of electrons, important in the folding and stability of proteins and the interactions between lipids in cell membranes (phospholipid bilayer)
• Disulfide bonds are covalent bonds formed between the sulfur atoms of two cysteine residues in proteins, contributing to the tertiary structure and stability of proteins (insulin)
• Hydrophobic interactions are the tendency of nonpolar molecules to aggregate in aqueous solutions to minimize their contact with water, playing a crucial role in the folding and stability of proteins and the formation of lipid bilayers in cell membranes (membrane proteins)