Cheese and Enzymes
Originally, cheese was made by killing a newly-born, milk-fed calf and remove its stomach to make rennet. The rennet was derived from the inner lining of the abomasum, the fourth stomach of the calf. After scraping the stomach, the cheesemaker would dry it in the sun by stretching it on a rack. After the stomach was dry, it was cut it into squares or strips. Before the strips or squares were used, they were soaked in cold water and washed thoroughly before being placed in milk. In an alternative process the strips or squares were dried, then ground, and finally mixed with a salt solution to extract rennin. Rennin is "a coagulating enzyme occurring in the gastric juice of the calf, forming the active principal of rennet and able to curdle milk." The cheese industry prefers a broader definition of rennin, calling it "any enzyme used for the controlled coagulation of milk."

What does rennin do?
Placed in milk, rennin or rennet breaks down a protein called kappa casein that keeps milk in liquid form. The breaking down of kappa casein leads to coagulation of the milk that will become cheese. Another term used for rennin is chymosin.
Not all cheese is made with animal-derived rennet. There are a number of rennetless cheeses whose coagulating enzymes are vegetable, microbial, or genetically engineered. One group of rennetless cheeses has acidic levels high enough not to require enzymes for coagulation. This group includes cottage cheese, ricotta, and some varieties of mozzarella. Rennetless has also become a generic term for any cheese made without any animal derived enzymes.
Chymosin, or rennet, is most often used for enzyme coagulation. During the primary stage, rennet cleaves the Phe(105)-Met(106) linkage of kappa-casein resulting in the formation of the soluble CMP which diffuses away from the micelle and para-kappa-casein, a distinctly hydrophobic peptide that remains on the micelle. The patch or reactive site, as illustrated in the above image, that is left on the micelles after enzymatic cleavage is necessary before aggregation of the paracasein micelles can begin.
During the secondary stage, the micelles aggregate. This is due to the loss of steric repulsion of the kappa-casein as well as the loss of electrostatic repulsion due to the decrease in pH. As the pH approaches its isoelectric point (pH 4.6), the caseins aggregate. The casein micelles also have a strong tendency to aggregate because of hydrophobic interactions. Calcium assists coagulation by creating isoelctric conditions and by acting as a bridge between micelles. The temperature at the time of coagulation is very important to both the primary and secondary stages. With an increase in temperature up to 40° C, the rate of the rennet reaction increases. During the secondary stage, increased temperatures increase the hydrophobic reaction. The tertiary stage of coagulation involves the rearrangement of micelles after a gel has formed. There is a loss of paracasein identity as the milk curd firms and syneresis begins.

Types Of Coagulating Enzymes Used To Make Cheese
Animal rennin is the coagulating enzyme (rennin or chymosin) that is harvested from the stomachs of calves.
Vegetable rennin is a misnomer given that the definition of rennet recognizes it strictly as an animal derived substance. Although cheese has been made using enzymes from the Lady Bedstraw, Stinging Nettle, and Thistle flower, the term vegetable rennet is most commonly used when describing enzymes produced using microbes. "Vegetable rennet" is sometimes used more generally to describe any non-animal rennet.
Microbial rennin are enzymes derived from a controlled fermentation of a fungus (e.g., Mucor Pusillus, Mucor Miehi, and Endothia Cryphonectria) or microbial rennets. However, microbial rennets cannot be used to produce cheddar or hard cheeses, limiting their application as an alternative to animal or bioengineered rennets.
Genetically engineered rennin Shortages and fluctuations in the available supplies of calf rennet prompted the development of genetically engineered rennet. Food scientists can however produce a continuous and pure source of microbial chymosin by incorporating a calf's prochymosin gene into a microorganism. The first microbial chymosin was affirmed GRAS (generally recognized as safe) by the FDA in 1989, with many others following shortly thereafter. Currently, it is estimated that 50% of the chymosin used is produced by transgenic means.
Rennetless. The term "rennetless" is used to mean two things in the cheese world. First, rennetless cheeses are also called "acid precipitated cheeses" and include cottage cheese, ricotta, and some mozzarella. These types of cheese are created using their natural acid levels and do not require the addition of a coagulating enzyme. The second interpretation of "rennetless" cheese is any cheese made without the use of animal derived coagulants.

The good and the Bad about Rennin
The use of rennin in cheese is controversial because of the way it is obtained. Here are some reasons why.
Animal rights. Animal rights activists argue that it is inhumane to kill calves for their stomach enzymes, especially when there are several alternative coagulants available to make cheese. These activists would argue that if you eat cheese, then purchase one that is made using cloned or microbial enzymes.
Vegetarianism. Vegetarians can have a confusing time trying to figure out what type of coagulant is acceptable in their cheese. While some vegetarians would strictly adhere to a non-dairy diet, others who eat dairy are content to allow microbial coagulants and some can accept cloned chymosin as a reasonable alternative to using calf rennet. Several vegetarian organizations accept the use of cloned animal enzymes as a reasonable alternative to the animal rennet derived from the killing of calves.
Bioengineering. Genetic engineering has brought new ways to create chymosin for use in cheese making. Originally, a prochymosin gene was injected into a host strain of E Coli K-12, creating a tiny enzyme factory that produced an extremely pure and recoverable chymosin for use in cheese production. Current technology cuts genes from a calf cell and injects it into the genomes of bacteria and yeast. This produces high quality chymosin that is not subject to the volatile market for animal derived rennet. It is estimated that 70% of domestic cheese is produced with bioengineered chymosin. For a consumer who does not want bioengineered foods, animal or microbial rennet should be their choice.
Religion. Some orthodox religions (Jewish and Islam) have specific requirements and prohibitions for the consumption of meat products that can preclude the use of animal rennet. For example, information received from Dr. Chaudry of the Islamic Food and Nutrition Council of America (IFNCA), stated that for a food to be "Halal" (permitted for consumption by Muslims), it must be void of certain animal products and processing procedures. In this case, cheeses that are made from animal rennet are only excluded if the calf is slaughtered improperly or is contaminated with other prohibited ingredients or procedures. The IFNCA recommends the use of microbial or bioengineered chymosin for cheese making.

Problems With Cheese Coagulants
Labeling. There is no requirement for a cheese ingredient label to distinguish between the types of rennet that it may or may not contain. In fact, a cursory review of cheese labels at our 6th and Lamar store in Austin, Texas revealed at least 8 different ways that the coagulating enzymes were identified. They include, enzymes, microbial enzymes, microbial enzymes (non-animal, rennetless), rennetless, rennet, enzymes and rennet, vegetarian rennet, and microbial coagulants. A significant portion of the surveyed cheese labels simply said enzymes, while several labels did not list the type of coagulant used at all.
Obviously this type of labeling hurts cheese buyers as well as consumers. For a store cheese buyer, it is a challenge to track down cheeses that list the type(s) of coagulants used, while for the consumer, buying cheese products with a full understanding of the ingredients is next to impossible. Some companies have taken the time to list whether the cheese they make contains a particular type of enzyme, but these are few and far between.
Enzyme mixing. Compounding the labeling problem is the fact that cheese producers can mix animal, plant, and microbial enzymes under one ingredient listing called "enzymes". The FDA determined that it would be impractical for individual cheese packers to have on hand all the variations of labels needed to properly designate all cheese enzyme mixtures.

WAIT! Cheese can even be made at home!
With today's technology, communications and new attitudes about doing things creatively, it is about where homebrewing was twenty years ago about to explode.
Cottage cheese can be made with equipment and raw materials found in any kitchen. More advanced cheeses require some additional equipment and raw materials but it can all be learned by anyone willing to make the effort. I would put it at about the same level of complexity as making beer or wine at home.



BARE BONES
Ingredients:
1 gallon 2% milk
1/2 cup vinegar
1 tsp salt

1. Heat the milk to 190F. You will need a thermometer for other cheeses but you can get by here turning off the heat just before the milk begins to boil.
2. Add the vinegar and allow the mixture to cool.
3. When cool, pour the mixture, into a colander and drain off the whey.
4. Pour the curds into a bowl and sprinkle on the salt and mix well. You may wish to use less salt or more. It is simply a matter of taste which is the next step. You can add a little cream for a silky texture.


Bibliography:
http://www.foodsci.uoguelph.ca/dairyedu/cheese.html
http://www.wholefoods.com/healthinfo/rennet.html
http://schmidling.com/making.htm