CHAPTER 1.1 BIOCHEMISTRY

Matter, Elements, Atoms & Molecules

  • Matter

    • Occupies space and has mass

    • Exists as elements in pure form and as compounds (fixed-ratio chemical combinations)

  • Elements

    • Cannot be broken down by chemical reactions

    • Composed of atoms; each element defined by its atomic number ZZ (number of protons)

    • Periodic-table layout: vertical columns = groups (similar valence), horizontal rows = periods (energy levels)

  • Compounds

    • Substances of two or more elements in a fixed ratio

    • Exhibit emergent properties distinct from constituent elements

The Elements of Life

  • Essential bulk elements (≈96%96\% of organism): C, H, O, N\text{C, H, O, N}

  • Remaining 4%4\%: P, S, Ca, K, Mg, Na, Cl\text{P, S, Ca, K, Mg, Na, Cl} etc.

  • Trace elements (minute quantities)

    • Examples: Fe, Zn, I\text{Fe, Zn, I}

    • Deficiencies cause disease

    • Nitrogen deficiency → stunted plants

    • Iodine deficiency → goiter in humans

Atomic Structure

  • Sub-atomic particles

    • Proton: +1+1 charge, mass ≈ 11 amu

    • Neutron: 00 charge, mass ≈ 11 amu

    • Electron: −1-1 charge, mass ≈ 1/18401/1840 amu, occupy electron shells

  • Atomic mass A=Z+NA = Z + N (protons + neutrons)

  • Neutral atoms: #\,e^- = #\,p^+

  • Energy levels / shells

    • Electrons possess potential energy; can change shells only by absorbing/losing quanta equal to level difference

    • First shell max 22 e⁻, second 88, third 1818 (focus on first $$18