Structural View of Biology
Enzymes are Nature's chemists, performing all of the chemical transformations needed for life. Enzymes catalyze chemical reactions by bringing together all of the necessary chemical tools in the proper place. They typically have an "active site" that captures the chemicals that will be modified, holding them in the perfect orientation to perform the chemical change. Researchers have separated the many types of enzymes into a few functional classes, based on the reactions that they perform.
Oxidoreductases - Shuffling Electrons
Oxidoreductases are experts in oxidation and reduction, where individual electrons are added or removed from molecules during a chemical reaction. The normal amino acids in proteins are not particularly effective for the management of electrons, so oxidoreductases often use special cofactors in their reactions, such as metal ions or prosthetic groups.
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Living with oxygen is dangerous. We rely on oxygen to power our cells, but oxygen is a reactive molecule that can cause serious problems if not carefully controlled. One of the dangers of oxygen is that it is easily converted into other reactive compounds. Inside our cells, electrons are continually shuttled from site to site by carrier molecules, such as carriers derived from riboflavin and niacin. If oxygen runs into one of these carrier molecules, the electron may be accidentally transferred to it. This converts oxygen into dangerous compounds such as superoxide radicals and hydrogen peroxide, which can attack the delicate sulfur atoms and metal ions in proteins. To make things even worse, free iron ions in the cell occasionally convert hydrogen peroxide into hydroxyl radicals. These deadly molecules attack and mutate DNA. One theory, still controversial, is that this type of oxidative damage accumulates over the years of our life, causing us to age.
Discussed Structurescatalasemanganese catalase
Hydrogen gas is an unusual substance. Normally, it is stable and must be coaxed with powerful catalysts to enter into chemical reactions. But when mixed with oxygen, a tiny spark will set off an explosive chain reaction. Hydrogen gas holds great promise to be the greenest of green energy sources. It has many advantages: compared with many fuels, it releases a lot of energy for its weight, and the reaction forms only energy and pure water. It has substantial disadvantages, however. It is dangerous to store, and it is difficult to perform the reaction in a controlled, non-explosive manner. Currently, the fuel cells being developed for use in hydrogen-powered vehicles use costly platinum catalysts to perform this reaction. Researchers are now looking to nature for other alternatives.
Discussed Structures[NiFe] hydrogenase[FeFe] hydrogenase[Fe] hydrogenase[FeFe] hydrogenase and cytochrome c
Nitrogen is needed by all living things to build proteins and nucleic acids. Nitrogen gas is very common on the earth, as it comprises just over 75% of the molecules in air. Nitrogen gas, however, is very stable and difficult to break apart into individual nitrogen atoms. Usable nitrogen, in the form of ammonia or nitrate salts, is scarce. Often, the growth of plants is limited by the amount of nitrogen available in the soil. Small amounts of usable forms of nitrogen are formed by lightning and the ultraviolet light from the sun. Significant amounts of nitrogen are fed to plants in the form of industrial fertilizers. But the lion's share of usable nitrogen is created by bacteria, using the enzyme nitrogenase.
The proteins that make up the skin, muscle, hair, bones and other organs in your body are primarily composed of a set of 20 building blocks, called amino acids. Amino acids are the alphabet in the protein language: when combined in a specific order, they make up meaningful structures (proteins) with varied and specific functions. Amino acids have distinct shapes, sizes, charges and other characteristics. Many amino acids are synthesized in your body from breakdown products of sugars and fats, or are converted from other amino acids by the action of specific enzymes. However, a few of them, called essential amino acids, cannot be synthesized or converted in your body and have to be obtained from the food you eat. Phenylalanine is one such essential amino acid. It is closely related to another amino acid, tyrosine, which just has an additional hydroxyl (OH) group. Liver cells contain an enzyme called phenylalanine hydroxylase, which can add this group and convert phenylalanine to tyrosine. Thus as long as this enzyme is functional and there is a reasonable supply of phenylalanine, tyrosine can be synthesized in your body and does not have to be included in the food that you eat.
Discussed Structuresphenylalanine hydroxylase catalytic domain
Our diet includes a wide variety of different molecules. Many of these molecules are broken down completely and used to generate the metabolic energy that powers our cells. Others are disassembled piece-by-piece and recycled to build our own proteins and nucleic acids. The ones that are left over are broken down and discarded. Xanthine oxidoreductase, shown here from PDB entry 1fo4, is the last stop for extra purine nucleotides (ATP and GTP) in our cells. Purines are broken down in several steps, ultimately yielding uric acid, which is excreted from the body.
Discussed Structuresxanthine oxidoreductaseurate oxidase
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