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Chemistry Foundation of Life: Matter, Atoms, and Bonding

Matter and the Chemistry Foundation of Life

  • Topic context: Chemistry foundations underpin biology; Chapter 2 focuses on what matter is and how atomic building blocks drive biological processes.
  • Matter and elements
    • Matter: composed of naturally occurring elements, each with a unique chemical symbol (as shown on the periodic table).
    • Compound: a substance consisting of two or more elements combined in a fixed ratio; example given: sodium chloride (table salt) forms a new compound with properties distinct from its constituent elements (sodium and chlorine).
    • Emergent properties: compounds exhibit features not found in the individual elements (e.g., NaCl has properties different from Na and Cl).
  • Relevance to biology
    • Living organisms are made of elements; understanding atom behavior helps explain biological processes.
    • Chemistry is essential to explain phenomena biologists study (e.g., metabolism, bonding, molecular interactions).
  • Abundance of elements relevant to life
    • Four most common elements in living organisms: Carbon (C), Oxygen (O), Hydrogen (H), Nitrogen (N).
    • Reported approximate mass contributions in life: C ~ 18%, H ~ 10%, N ~ 3% (O’s percentage is implied but not listed in the spoken slide content).
    • Environment vs life composition differences:
    • Atmosphere: about 21% O₂, most nitrogen, trace carbon and hydrogen.
    • Earth's crust: high oxygen, carbon and hydrogen in trace amounts.
    • Living organisms: O, C, H, N make up about 96.3% of body mass; remaining ~3.7% includes Ca, P, K, etc., with trace elements making up <0.01% (examples: boron, copper, iodine, iron).
    • Importance of trace elements
    • Although present in tiny amounts, trace elements are essential for life; deficiencies can cause disease (e.g., iodine deficiency leading to enlarged thyroid).
  • Element deficiencies in plants and humans (examples from the transcript)
    • Iodine deficiency: essential for thyroid hormone production; deficiency leads to enlarged thyroid (goiter).
    • Plant nitrogen deficiency: signs include yellowing of older leaves (chlorosis); nitrogen is needed to form amino groups in proteins and to support chloroplast function.
    • Iron deficiency: highlighted as important for various biological processes (the speaker phrased it as related to cancer in the transcript; note this may be a misstatement in the spoken content and is not typically described as iron being required for cancer in standard depictions).
  • What’s inside matter: atoms and their composition
    • Atom: smallest unit of matter that retains the properties of an element.
    • Subatomic particles and charges
    • Neutrons: neutral
    • Protons: positive charge
    • Electrons: negative charge
    • Atomic models demonstrated in class
    • Nucleus model (protons and neutrons in a small central region) vs. electron cloud model (electrons depicted as a probability cloud rather than fixed orbits).
    • The cloud model better reflects quantum behavior: electrons occupy regions of space with probability rather than exact circular paths.
  • What makes atoms different
    • Elements differ by the number of subatomic particles:
    • Protons (positive charge) determine the identity (atomic number, Z).
    • Neutrons (neutral) contribute to mass and isotopes.
    • Electrons (negative) determine chemistry and bonding.
    • An atom’s identity is defined by its number of protons; atoms of the same element can have different numbers of neutrons (isotopes).
  • Atomic number, mass number, and isotopes (illustrative example with carbon)
    • Periodic table notation example for carbon:
    • Atomic number: Z = 6 (number of protons)
    • Mass number: A (sum of protons and neutrons)
    • Mass and mass units
    • Mass of an atom is primarily from protons and neutrons; electrons contribute negligibly to atomic mass.
    • Atomic mass unit (amu) is used to express atomic and molecular masses; 1 amu is defined relative to carbon-12.
    • Mass number concept: for carbon, common isotopes include
      • Carbon-12: Z = 6, A = 12 (stable)
      • Carbon-13: Z = 6, A = 13 (stable)
      • Carbon-14: Z = 6, A = 14 (radioactive)
    • Isotopes
    • Isotopes are atoms of the same element with the same number of protons but different numbers of neutrons.
    • Carbon-12 vs Carbon-13 vs Carbon-14 illustrate isotopes with differing masses but identical chemical behavior (chemistry largely depends on electrons).
    • Radioactive isotopes are unstable and decay over time, emitting radiation.
  • Radioactive isotopes and their uses
    • Radioactive isotopes are not inherently