Amino acids as the monomers of proteins

1. An amino acid is the monomer from which every protein is built, and a protein is the polymer that results from joining them.
2. Amino acids contain carbon, hydrogen, oxygen and nitrogen, and a few of them contain sulfur as well.
3. Nitrogen is what sets proteins apart from carbohydrates and lipids, which contain no nitrogen at all.
4. There are about twenty different amino acids available to a cell, and each one has a different side group attached to the same basic structure.
5. Because the basic structure is the same in every amino acid, any one of them can be joined to any other, in any order.
6. The sequence, meaning the order in which the amino acids are joined, is different for every different protein.
7. A short chain is called a polypeptide, and a protein is one or more of those chains folded into its finished shape.
8. Even a small protein of a hundred amino acids can be assembled in an almost unimaginable number of different orders, which is why one set of twenty monomers can build every protein a body needs.
9. A plant makes all its own amino acids by combining sugars with nitrates taken up from the soil, while an animal has to obtain most of its from protein in food.

Building and breaking proteins

1. Amino acids are joined by condensation reactions, and each new bond releases one molecule of water.
2. Joining $n$ amino acids into a single chain therefore forms $n-1$ bonds and releases $n-1$ molecules of water.
3. The joining happens on the ribosomes, and the energy needed for it comes from ATP supplied by respiration.
4. Hydrolysis breaks a protein back down, adding one molecule of water at each bond to release the individual amino acids again.
5. Protease enzymes hydrolyse the protein in food during digestion, because a whole protein molecule is far too large to be absorbed.
6. The amino acids released are absorbed into the blood and delivered to cells, which then join them together in a completely new order to build the proteins that body needs.
7. A protein eaten in a meal is therefore not used as it is; it is taken apart into its monomers and those monomers are reassembled.
8. Amino acids cannot be stored, so any that are surplus to requirements are broken down in the liver rather than kept for later.
9. Proteins in the body are also being hydrolysed and rebuilt all the time, which is why a steady supply of amino acids is needed even in an adult who is no longer growing.

Folding gives each protein its shape

1. Once the chain has been assembled it does not stay stretched out; it folds into a particular three-dimensional shape.
2. The folded shape is held in place by bonds between different parts of the same chain, formed wherever two side groups come close enough to attract one another.
3. Which side groups end up close together depends entirely on the sequence, so the sequence determines the shape.
4. A different sequence brings different side groups together, folds into a different shape, and therefore produces a protein that does a different job.
5. Most proteins work by binding to another molecule, and binding only happens when the two shapes are complementary, which means they fit together.
6. An enzyme is a protein whose folded shape leaves a pocket called the active site, and only a substrate with a matching shape will fit into it.
7. The same principle explains why an antibody binds to one pathogen and not another, and why a receptor in a cell membrane responds to one hormone only.
8. Structural proteins are shaped for strength instead of binding, which is how collagen makes tendons tough and keratin makes hair and nails hard.
9. Carrier proteins in a cell membrane are folded so that a channel runs right through them, which is what lets particular substances pass into and out of the cell.

What happens when a protein loses its shape

1. Denaturation is the permanent change in a protein's folded shape that happens when the bonds holding the fold together are broken.
2. A high temperature breaks those bonds because the chain vibrates so strongly that the weak attractions between side groups cannot hold.
3. An extreme pH breaks them because it changes the charge on the side groups, so groups that were attracting each other no longer do.
4. Once the fold is lost the chain takes up a different shape, and the binding site it used to carry no longer fits the molecule it was built for.
5. The sequence of amino acids is not affected, because the bonds joining the amino acids into a chain are much stronger than the ones holding the fold.
6. Denaturation is not reversible, so a denatured protein cannot be cooled or neutralised back into working order.
7. You see it happen every time an egg is fried, because the clear runny protein in the white turns solid and white as it denatures and does not turn back.