"Against stupidity the gods themselves fight in vain." -- Johann von Schiller

I. What is life made of?

1. The German chemist Friederich Wöhler made the compound urea in his laboratory in 1828.
   1. Urea is a waste product found in mammal urine. . . but Wöhler made urea starting with chemicals that had never been part of a living thing.
   2. Who cares?
      1. Many scientists at the time thought that life was caused by some "vital force" which made living matter fundamentally different from nonliving matter.
      2. Wöhler's experiment -- and countless more that followed -- showed that living things aren't different from nonliving things at the chemical level. The same atoms are found in both, and both follow the same basic laws of chemistry.
      3. Living things are chemically very complex, much more complex than typical nonliving things -- but this is a difference of degree, not of kind.
2. By 1800, chemists had discovered many ways to break down substances found in nature, and to create new substances.
   1. Some substances could not be broken down into anything else. They might combine to make new materials, but they could not be broken down into anything simpler.
   2. These are the chemical elements.
   3. Common examples include: gold, silver, copper, aluminum, iron, sulfur, carbon, oxygen, helium. . .
      1. There are now known to be 88 elements found in nature.
      2. Four of them -- carbon, nitrogen, oxygen, and hydrogen (CHON)-- make up over 95% of your body. Two others -- sulfur and phosphorus (SP) are also very important.
      3. Others (iron, calcium, potassium, zinc, etc.) play subordinate but still important roles.
      4. There is a standard system for abbreviating elements. Usually, but not always, we use the first letter or first two letters of the element's name. Examples: carbon = C; hydrogen = H; oxygen = O; nitrogen = N; helium= He; neon = Ne; gold = Au (from its Latin name aurum). . . and so on. Check out this table of the elements if you want more information. . .
3. Chemists like John Dalton (1803) noticed that elements combined with other elements to make compounds -- new substances with very different properties -- but only in fixed ratios of small whole numbers. Different compounds are made of different ratios of elements.
   1. Simple example: If you send an electric current through some water, you will break it up into hydrogen and oxygen. . .
   2. . . . and you will always get exactly twice as much hydrogen as oxygen, no more and no less.
4. What this suggests is that elements are made up of atoms -- tiny particles which can attach to each other, but only in specific and definite ways. (An attachment between two atoms is a chemical bond, and we'll cover those shortly.)
   1. Two hydrogen atoms can stick to one oxygen atom, and that gives you a molecule of water. (We write this as the familiar H₂O.)
   2. You can also stick two hydrogen atoms to two oxygen atoms, but that does not give you water. It gives a compound known as hydrogen peroxide, H₂O₂ (used to disinfect cuts and wounds, and to bleach hair, among other things).
   3. Conclusion: A compound is determined by the numbers, arrangements, and types of atoms that make it up. Change that, and you change the compound.

1. Around 1900, radioactivity was discovered.
   1. Some atoms aren't stable -- they break up, and throw out "pieces" of themselves.
   2. Other atoms are usually stable but can be forced to break up.
   3. The "pieces" -- radiation and subatomic particles -- "thrown out" by atoms breaking up can be detected as radioactivity.
   4. And the upshot is that atoms aren't indivisible -- they can be broken into even smaller pieces.
2. By 1935, scientists had isolated and named the "pieces", a.k.a. subatomic particles.
   1. Three kinds of stable subatomic particles make up atoms:
      1. Proton -- a particle with a positive electric charge
      2. Electron -- a particle with a negative electric charge
      3. Neutron -- a particle with no electric charge
   2. The number of protons (the atomic number normally equals the number of electrons. If it doesn't--if an atom is missing an electron, or it has an extra -- the atom has an electric charge on it, and is called an ion.
3. OK, but how are these particles arranged in an atom?
   1. Old "plum pudding" model had all three types of particles clumped together, forming a sort of lump.
   2. Famous experiment by Ernest Rutherford disproved this model. Rutherford showed that an atom is mostly empty space. (!?!)
   3. The protons and neutrons are clustered together in the center, or atomic nucleus,
   4. . . . . while the electrons are whizzing around the nucleus in orbits.
   5. If you could somehow enlarge an atom to the size of the Louisiana Superdome in New Orleans, the electrons would be whizzing around the roof, and the nucleus would be the size of a pea on the 50-yard-line. Most of an atom is empty space.
   6. But electrons don't just orbit anywhere. They can only exist at certain energy levels, called orbitals. (Analogy: You can only live on the first, second, third, etc. floor of a building; there is no such thing as a one-half floor, 2.35th floor, 3.14159th floor.)
   7. "Solar system" model of an atom looks like this. Notice that the electrons are in one of two orbitals:
      
      This represents an atom of carbon-12: six protons, six neutrons, six electrons

   8. From the point of view of a nuclear physicist, this is not really an accurate model. Atoms don't "really look" like this (the nucleus is WAYYYYY too big, and the orbitals of electrons are NOT neat circles). However, it clearly shows those features of an atom that we will need to apply to biology.
4. Chemical Bonding
   1. Each orbital can only accommodate a set number of electrons.
   2. However, atoms can share electrons between outer orbitals, so that both fill the available spaces in their outer orbitals.
   3. A bond between atoms that's caused by sharing electrons is a covalent bond
   4. Example: This is a molecule of methane, the main ingredient in natural gas (formula CH₄):
   5. Covalent bonds can be drawn as short lines: . When there's no confusion possible, the lines can be left out: CH₄.
      c. Your text also uses "bubble diagrams" to represent molecules. Methane would look like this:

      

      Most of the molecules we will be interested in are held together by covalent bonds, and most of the chemical reactions we will study involve breaking and reforming covalent bonds.