Core Concepts
In this article, you will learn about the functions, mechanics, and types of one of the most important biomolecules: enzymes.
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What Are Enzymes?
Enzymes are a class of biomolecules responsible for catalyzing chemical reactions in cells. Enzymes make life possible, as they allow for many of the most important biochemical changes in cells. Indeed, without enzymes, crucial processes such as cellular respiration, photosynthesis, and protein synthesis would not occur. In fact, the utility of enzymes allows them to be used in processes important in research, such as molecular cloning and PCR.
The majority of enzymes are proteins. These enzymes are made of amino acids linked together by peptide bonds, like all proteins. Like all proteins, enzymes may denature in extreme conditions. However, there exist many enzymes that are instead made of ribonucleic acids (RNA), which biochemists call “ribozymes”. Interestingly, many enzymes are primarily made of amino acids but may have additional attaching components made from metal cations or organic material that serve important roles in the function of the enzyme. Biochemists call the organic non-protein structural components “prosthetic groups”.
Aside from prosthetic groups, enzymes may also require molecules to participate in a reaction aside from the principal reactant, called “cosubstrates.” Collectively, biochemists use the term “cofactor” to encompass cosubstrates, prosthetic groups, and metal cations used by enzymes.
Enzymes, as a group, have extensive structural diversity, and biochemists have observed enzymes in a variety of shapes and sizes. This diversity reflects the broad range of functions that enzymes serve, due to the vast amount of chemical reactions necessary for life.
What Do Enzymes Do?
As mentioned before, enzymes perform the important function of reaction catalysis. In other words, enzymes make it easier for slow, rate determining reactions, which speeds up the overall reaction chain. The way enzymes serve this purpose relates directly to their structure.
The Active Site
All enzymes have an important structure called an active site, to which their desired reactants bind. Organisms tend to build enzymes to perform one specific reaction, meaning that an enzyme’s active site only needs to bind to the reactants of their reaction and nothing else. Because of this, an enzyme’s active site generally has high substrate specificity, meaning that only their reaction’s reactants are chemically capable of binding to the active site. “Substrate” is the technical term biochemists use to describe the desired molecules that bind to an enzyme.
Additionally, since an enzyme’s substrate specificity comes from the chemistry of its active site, the enzyme’s substrate must bind in a specific orientation. The substrate’s chemical groups must interact with those of the active site in a specific way to bind to the enzyme.
Since the active sites only bind substrates of a particular orientation, this allows enzymes have specificity for certain stereoisomers of chiral substrates.
Once substrate fills the active site, the enzyme’s conformation, or its biochemical structure, then changes. This shifts the substrates to easily allow for the desired reaction to then take place.
Generally, enzyme-catalyzed reactions involve both breaking and forming chemical bonds. To do this, the enzyme’s conformation change tends to involve enzyme structures separating parts of a molecule to break bonds and joining together other structures to form bonds.
The Transition State
As mentioned before, enzymes speed up reactions by maneuvering substrates for the greatest ease of reaction. Chemists understand this phenomenon by looking at the reaction’s “transition state”. However, rather than being an isolable molecule, the transition state instead represents some necessary stage between product and reactant that only exists for one instant.
All reactions have a transition state, and the chemistry of this state determines their rate. Due to its short-lived nature, transition states tend to have much higher energy and much less stability than both their products and reactants. Therefore, even if a reaction involves the net release of energy from reactants to products, the reactants still need to absorb some energy for the reaction to start. Chemists generally depict this using an energy diagram, where reactants must climb a hill of energy to reach the transition state, before lowering in energy to form the products.
Here’s where enzymes come in. The structure of an enzyme’s active site is designed specifically to stabilize the transition state. Often, the enzyme does this by shielding the most reactive and unstable groups with complementary groups in the active site.
By stabilizing the transition state, the enzyme brings down the overall its overall energy. This then lowers the energy barrier of the reaction, allowing it to proceed at faster rates. As mentioned before, this catalysis allows important biochemical reactions to occur at a rate fast enough for life to exist. The steady state approximation applies to most enzyme-catalyzed reactions.
What Are Some Examples Of Enzymes?
Enzymes represent a diverse group of proteins, due to the wide variety of biochemical reactions that they catalyze in organisms. Biochemists use the suffix “-ase” to denote enzymes. Many of the most important enzymes fall into one of these six broad groups:
- Transferases, which catalyze reactions involving the transfer of a chemical group between molecules.
- Examples: Acetyltransferase, Methyltransferase, Peptidyl Transferase.
- Hydrolases, which catalyze hydrolysis reactions, breaking down large polymer molecules using water.
- Examples: Amylase, Lipase, Protease.
- Oxidoreductases, which catalyze redox reactions.
- Examples: Catalase, NADPH Oxidase
- Lyases, which catalyze elimination reactions that form carbon-carbon double bonds.
- Examples: Aldolase, Dehalogenase
- Ligases, which catalyze bond-forming reactions using ATP.
- Examples: DNA Ligase, Aminoacyl tRNA Synthetase, Ubiquitin Ligase
- Isomerases, which catalyze reactions that convert molecules into different isomers.
- Examples: Racemase, Isomerase.
