Atoms are the building blocks of life, forming elements and compounds essential for biological processes. Understanding their structure and properties is crucial for grasping how molecules interact and function within living organisms.

Chemical bonding shapes the behavior of atoms, creating diverse molecular structures. From simple molecules to complex macromolecules, these bonds determine the properties and functions of biological components, influencing everything from cell membranes to genetic material.

Atomic Structure and Properties

Fundamentals of matter and elements

• Matter occupies space and has mass
  • Composed of elements, simplest forms of matter that cannot be broken down chemically (carbon, oxygen, hydrogen, nitrogen)
• Elements defined by atomic number, number of protons in nucleus
  • Carbon, oxygen, hydrogen, nitrogen most abundant elements in living organisms
• Elements combine to form compounds, building blocks of biological molecules
  • Water (H2O), carbon dioxide (CO2), glucose (C6H12O6) are biologically important compounds
• Elements are organized in the periodic table based on their properties and atomic structure

Atomic structure and properties

• Atoms are basic units of elements composed of protons, neutrons, electrons
  • Protons have positive charge, located in nucleus
  • Neutrons are electrically neutral, also located in nucleus
  • Electrons have negative charge, orbit nucleus in energy levels or shells
• Number of protons in atom determines atomic number and identity
• Isotopes are atoms of same element with different numbers of neutrons
  • Isotopes have same chemical properties but different atomic masses (carbon-12, carbon-13, carbon-14)
• Electron configuration influences atom's chemical reactivity and bonding properties
  • Valence electrons in outermost shell participate in chemical reactions and bonding (sodium, chlorine)
• Electrons occupy specific orbitals within energy levels, determining atomic behavior

Atomic mass and measurement

• Atomic mass is measured in atomic mass units (amu)
• Mass of an atom is primarily determined by its protons and neutrons

Chemical Bonding and Molecular Structure

Electron donation vs sharing

• Chemical bonds form when atoms interact to achieve more stable electron configuration
• Ionic bonds involve complete transfer of electrons from one atom to another
  1. Typically occurs between metals and nonmetals (sodium chloride NaCl)
  2. Results in formation of positively and negatively charged ions (Na+, Cl-)
• Covalent bonds involve sharing of electrons between atoms
  1. Typically occurs between nonmetals (hydrogen H2, oxygen O2)
  2. Single, double, triple bonds can form depending on number of electron pairs shared
• Polar covalent bonds form when electrons are shared unequally between atoms
  • Occurs when there is difference in electronegativity between bonded atoms (water H2O)
  • Results in formation of partial positive and negative charges within molecule

Molecular properties and interactions

• Electronegativity is the ability of an atom to attract electrons in a chemical bond
• Polarity of molecules is determined by the distribution of charge due to differences in electronegativity
• Some molecules can have multiple stable electron configurations, known as resonance structures

Elements in biological structures

• Molecules formed when two or more atoms held together by chemical bonds
  • H2, O2, N2 are simple molecules
• Macromolecules are large, complex molecules formed by polymerization of smaller subunits
  • Proteins, carbohydrates, lipids, nucleic acids are four main classes of biological macromolecules
• Monomers are building blocks of macromolecules
  • Amino acids are monomers of proteins
  • Monosaccharides are monomers of carbohydrates (glucose, fructose)
  • Fatty acids and glycerol are monomers of lipids
  • Nucleotides are monomers of nucleic acids (DNA, RNA)
• Macromolecules assemble to form progressively complex biological structures
  • Proteins and lipids form cell membranes
  • Nucleic acids (DNA and RNA) store and transmit genetic information
  • Carbohydrates and proteins form extracellular matrix (collagen, elastin)