"One of the advantages of being disorderly is that one is constantly making exciting discoveries ." -- A. A. Milne

I. Cell structure

1. Prokaryotic cells
   1. The DNA is usually clumped in the center, in an area called the nucleoid, but it's not partitioned off from the rest of the cytoplasm with a membrane, so it's not a nucleus.
   2. Prokaryote DNA is organized into a large loop and several smaller loops (plasmids). Plasmids may be copied and transferred between bacteria, which is pretty much what passes for sex among bacteria.
   3. The rest of the cell is organized very simply. The organelles found in a eukaryotic cell do not exist in prokaryotes. . .
      1. . . . except for ribosomes, which generally float freely within the cell. . .
      2. . . . and sometimes simple folds or sacs of membrane inside the cell.
   4. Most prokaryotes, though not all, have a cell wall outside the plasma membrane
2. Eukaryotic cells -- which include almost every living thing you're familiar with, including you yourself -- are more complex.
   1. The DNA is partitioned off from the rest of the cytoplasm and held in a double membrane sac, the nucleus.
      1. Holes in the nuclear membrane are known as nuclear pores.
      2. A portion of the nucleus which usually looks darker than the rest, the nucleolus, is the site where ribosomes are made.
   2. Several internal organelles, all made up of membrane and all interconnected, function in synthesizing, packaging, transporting, and storing macromolecules. (Collectively they're sometimes called the endomembrane system.) These include:
      1. Endoplasmic reticulum (abbreviated ER), an internal network of folded membranes. Some of the ER is studded with ribosomes (rough ER), while the rest is not (smooth ER). Rough ER is the site of much protein synthesis, while lipids, carbohydrates, etc. are made on the smooth ER.
      2. The Golgi complex, a small stack of flat membrane sacs (looking a bit like a stack of pancakes). This functions as a sort of "shipping department" or "packaging center" for the cell.
      3. Vesicles, smaller sacs that store and transport molecules. A very important type of vesicle is the lysosome, which contains digestive enzymes. Similar to vesicles, just larger, are vacuoles, which often function in pumping excess water out of the cell, or in storage.
      4. Why did I say these are interconnected? Because a vesicle might bud off, say, the ER, travel to the Golgi body, and fuse with it. Another vesicle might bud off the Golgi and remain a separate vesicle, or fuse with the ER, or even fuse with the external plasma membrane. . .
   3. Mitochondria and, in some eukaryotes, chloroplasts
      1. Mitochondria are the "powerhouses of the cell," because it's there that energy is generated (in the form of a nucleotide called ATP -- more to follow!)
      2. Chloroplasts are the sites of photosynthesis -- the making of sugar from carbon dioxide and water, using solar energy -- in those eukaryotes that have them.
      3. Both mitochondria and chloroplasts contain an outer and an inner membrane. The inner membrane is folded into complex folds or pinched off into sacs.
      4. What's more, both mitochondria and chloroplasts have their own DNA -- which is in a loop, not a linear piece! The DNA sequences of these organelles are more like bacterial DNA than eukaryote DNA! What's more, a cell cannot make more of either on its own! This is powerful evidence for serial endosymbiosis theory: both mitochondria and chloroplasts are descended from bacteria which once entered an ancestral eukaryotic cell, and the two became mutually dependent. (Kudos to Lynn Margulis for figuring this out about twenty-five years ago. . .)
   4. The cytoskeleton, a network of filaments made up of protein.
   5. Eukaryotic cilia and flagella are thin hair-like organelles sticking out of the cell and able to move back and forth.
      1. The only real difference between these is that cilia are shorter than flagella. Their structures are the same. Just to make things confusing, you may see both referred to as undulipodia.
      2. Cilia and flagella may either allow the cell to move through fluid -- as in sperm cells -- or move fluid past the cell -- as in the ciliated cells in your lungs that move mucus through your respiratory tract.