Atoms are the building blocks of life, made up of protons, neutrons, and electrons. These subatomic particles determine an atom's properties and behavior. Understanding their arrangement is key to grasping how atoms interact and form chemical bonds.

Chemical bonding is crucial for creating biological molecules. Different types of bonds, like ionic, covalent, and hydrogen bonds, hold atoms together in various ways. These bonds shape the structure and function of important molecules in living organisms.

Atomic Structure and Subatomic Particles

Subatomic particles in atoms

• Atoms consist of three primary subatomic particles that determine their chemical properties
  • Protons carry a positive charge and are located in the dense central nucleus of the atom
    • The number of protons defines the atomic number, which uniquely identifies each element (hydrogen has 1 proton, helium has 2)
  • Neutrons have no electrical charge and reside in the nucleus alongside protons
    • Neutrons contribute to the atom's mass but do not influence its chemical behavior
  • Electrons possess a negative charge and orbit the nucleus in electron shells or energy levels
    • The number of electrons in an atom determines its chemical reactivity and bonding characteristics
    • Valence electrons, found in the outermost electron shell, actively participate in chemical bonding (atoms with 1 valence electron like sodium are highly reactive)
• Isotopes are variants of an element with differing numbers of neutrons
  • Isotopes exhibit identical chemical properties but have different atomic masses due to the varying neutron count (carbon-12 and carbon-14 are isotopes of carbon)

Electron configuration and reactivity

• Electron configuration describes the distribution of electrons in an atom's electron shells and subshells
  • Electrons occupy orbitals in a predictable sequence, progressing from the lowest to the highest energy levels (1s, 2s, 2p, 3s, etc.)
  • Orbitals are organized into energy levels (shells) and sublevels (s, p, d, f) based on their shape and orientation
• Valence electrons in the outermost shell govern an atom's chemical reactivity and bonding tendencies
  • Atoms with a complete valence shell (typically 8 electrons, except for the first shell which holds 2) are relatively stable and less reactive (noble gases like neon have full valence shells)
  • Atoms with incomplete valence shells display higher reactivity and readily form chemical bonds to attain a stable electron configuration (halogens like chlorine have 7 valence electrons and are highly reactive)
• The number of valence electrons dictates an atom's bonding patterns
  • Atoms with 1, 2, or 3 valence electrons are inclined to form positively charged cations by losing electrons (metals like sodium and magnesium)
  • Atoms with 5, 6, or 7 valence electrons tend to form negatively charged anions by gaining electrons (nonmetals like oxygen and sulfur)
  • Atoms with 4 valence electrons can either share electrons in covalent bonds or participate in ionic bonding (carbon forms covalent bonds, while silicon can form ionic or covalent bonds)

Chemical Bonding in Biological Molecules

Types of chemical bonds

• Ionic bonds form through the electrostatic attraction between oppositely charged ions (cations and anions)
  • Ionic bonds result from the transfer of electrons from one atom to another, creating charged particles
  • These strong bonds contribute to the stability of ionic compounds, such as sodium chloride (table salt)
  • Ionic bonds play a role in maintaining the structure and function of some proteins and in the formation of mineralized tissues (bones and teeth)
• Covalent bonds arise from the sharing of electrons between atoms
  • Covalent bonds can be single (sharing one electron pair), double (sharing two electron pairs), or triple (sharing three electron pairs)
  • These strong bonds hold atoms together within molecules and are essential for the formation of biological macromolecules (proteins, nucleic acids, and lipids)
• Hydrogen bonds are weak electrostatic attractions between a hydrogen atom bonded to an electronegative atom (nitrogen, oxygen, or fluorine) and another electronegative atom
  • Hydrogen bonds form due to the unequal sharing of electrons in a polar covalent bond, creating a slightly positive hydrogen and a slightly negative electronegative atom
  • Although individually weak, hydrogen bonds collectively contribute to the structure and function of biological molecules
  • Hydrogen bonds are crucial for the secondary structure of proteins (alpha helices and beta sheets), base pairing in DNA, and the unique properties of water

Molecular polarity in biological systems

• Polarity describes the uneven distribution of charge within a molecule
  • Polarity arises from differences in electronegativity between atoms in a covalent bond, creating a slightly positive and slightly negative end (dipole moment)
  • Polar molecules interact with other polar molecules and charged particles through electrostatic attractions
  • Polar molecules are hydrophilic (water-loving) and can form hydrogen bonds with water and other polar molecules, allowing them to dissolve in polar solvents like water
• Nonpolar molecules have a uniform distribution of charge and lack a dipole moment
  • Nonpolar molecules are hydrophobic (water-fearing) and do not form hydrogen bonds with water
  • In aqueous environments, nonpolar molecules tend to aggregate together due to the hydrophobic effect, minimizing their contact with water
• Molecular polarity plays a vital role in numerous biological processes
  • Cell membrane structure: phospholipids have a polar head and nonpolar tails, enabling them to form bilayers with a hydrophobic interior and hydrophilic exterior
  • Protein folding: the spatial arrangement of polar and nonpolar amino acids determines the three-dimensional structure and function of proteins
  • Enzyme-substrate interactions: polar and nonpolar regions of enzymes and substrates facilitate specific binding and catalysis, ensuring efficient biochemical reactions