There are many chemical processes at work when preparing our food, cooking our food and preserving our food. It goes beyond the intent of this posting to extensively cover all the known processes and reactions (and there are many not fully understood yet). But there are several that you need to be aware of:
Enzymatic reactions are reactions catalyzed by enzymes, the so-called bio-catalysts. These are active when the conditions are suitable. The enzymes have an optimum temperature and may be inactivated at higher or lower temperatures beyond the range. They also have optimum acidity levels (pH) where they are most active. Enzymes are responsible for deteriorating our food, but other enzymes are at work to make delicious dishes as well and some work to preserve our food! Examples: Fish, squid and shrimp that are not yet gutted, (in the case of shrimp that means the head is still on) are prone to decay, that is the gut enzymes work on the flesh to deteriorate the quality. Even freezing them before cleaning, reduces their shelf-life. In general fish are cold blooded: reducing the water temperature causes their body systems to adjust, but not necessarily immediately kills them. Other well- known examples are the conversion of starch from grains into sugar (bread baking; making of beer wort); the making of cheeses and the enzymatic action that involves fermenting fish, vegetables and beans into things like fish sauce, sauerkraut and bean curd, and the browning of peeled apple and avocado (see below, item 4).
The Maillard reaction is the reaction between reducing sugars and amino acids at higher temperatures, causing browning of food and creating the lovely taste of baked and fried crusts. Sometimes the cook adds some sugar to create more browning at lower temperatures (for example in barbequed spare ribs or roast duck in the Cantonese cuisine) or the cook takes effort to take the source of sugars away (washing away of starch, the precursor of sugars in cut potato strings or fries), in order not to create very dark colored French fries or potato chips at higher frying temperature.
Caramelization of sugars is purely heat induced and also causes browning and odor and taste changes.
Oxidation reactions: The oxidation of unsaturated oils and fats. Oily fish has a high amount of liquid poly-unsaturated oils and oxidation reactions have to be controlled to a minimum by keeping the cleaned fish very cold on ice. Beef fat that is solid at room temperature and is mostly unsaturated, can hardly be oxidized and can be kept at ambient temperature for a day with ease. Poultry is somewhere in between. Similarly, ground seeds or nuts with high poly-unsaturation best be stored in the freezer. Another example of oxidation reactions is sliced apples get brown quickly, especially those with a low acid content; mashed or cut avocado exhibits the same. The latter are enzyme catalyzed oxidation reactions and a squeeze of lemon or lime juice will help, and covering it with foil on the surface and placing it cool will also help. Sometimes blanching will also inhibit these browning reactions.
Starch gelatinization, protein denaturization and colloidal stability: these are physico-chemical reactions, actually no other molecules get formed, but the texture and form is affected and thus the presentation, mouthfeel and taste is changed. Starch molecules when in contact with water unfold and form a network at elevated temperatures. Depending on where the starch is derived from (potato, wheat, tapioca root etc) the gelatinization temperature is somewhat different. When baking bread the inside temperature of the bread should go slightly above the gelatinization temperature of the starch, otherwise the bread will not become firm and will not taste well. It is also observed when starch based sauces thicken. Other examples of colloidal reactions are the cooking of an egg, the curding of milk or cream upon the addition of acid, the thickening of vegetable based soups upon the action of an immersion blender, the making of mayonaise etc.