In order to actually be useful, protein chains need to fold up into their final shapes. Now, remember how yesterday I told you about how amino acids have side chains with different chemical properties? Some of these come into play here, for instance, two cysteines can bind to each other through a disulphide bond* (the same is not true of any other amino acid under normal cellular conditions). Other important factors that come into play are hydrophobicity (how much an amino acid repels water), whether it is negatively, neutrally or positively charged, and how much space it takes up. Hydrophobic and hydrophilic amino acids will tend to bunch together in like-minded groups, and obviously positive and negative charges are attracted to each other.
Linked here is an example diagram of a simple protein structure: http://users.soe.ucsc.edu/~pinal/p1/com
An awful lot of computing resources are currently going into trying to predict what shape a protein will be when folded from its sequence. We are really not very good at doing that from scratch yet, but what we do have is a large database of protein structures that have been solved using spectroscopic methods. So what we do is predict structures (and therefore often functions, too) by comparing the sequence of a newly discovered protein with already known similar ones in the databases, and extrapolating.
Protein structure is, of course highly related to function. A protein that forms a pore or transport channel in a cell membrane will by necessity have a hole through the middle, and myosin, the major component of muscle fibres, is long and thin. Something else very important about proteins is that many can be induced to undergo conformational changes, for example by binding to a small molecule. This is a fundamental aspect of molecular biology that is outside the scope of this series, but it should be obvious that a protein that floats around the cell quite happily and then changes shape (in order, say, that it can then bind to DNA) when a hormone is bound to it is a very useful signalling mechanism.
So... where are proteins found? The answer is, basically, everywhere. Proteins are the "building blocks" of all life- they make up large parts of your organs, your skin, your muscles. And they also tell the body where to put all the other bits that *aren't* proteins- all the fat, the bone, the energy stores, and when to release them again. They make up the scaffolds that hold your DNA, and they even control making more of themselves. Proteins are fundamental.
From all this you should be able to deduce that proteins folding up into the correct shape is very important. And you'll be unsurprised to hear that proteins folding up *wrongly* can be a cause of disease. The most famous examples of this are diseases such as BSE (aka Mad Cow Disease), which wrecks the brain through buildup of misfolded proteins which eventually cause tissue damage and cell death... and you can't function with spongy holes in the brain. The reason thes misfolded proteins, known as prions, are so nasty is that they can find other molecules of the protein they are the misfolded version of and turn them into copies of themselves. This, of course, is how BSE was spread- by feeding cows central nervous tissue from other, diseased cows.
So, at the end of the first week, we know what DNA is, and how it's stored and copied. We know how DNA instructs the body to make proteins, and we know that proteins are what makes you *you*. So with that groundwork under our belts, we can now start to look at variations between individuals of the same species, learn to use the horrible words "dominant" and "recessive" properly, and explain genetic diseases!
*Again, you do not need to know what one of these is. For the chemists among you, in oxidising conditions, such as those usually found in a cell, the two -SH groups on two cysteines will bond together to form -S=S- , one of the few chemical (as opposed to electrostatic or hydrogen) bonds in the higher structure of a protein.