Enzyme Biochemistry - What Enzymes Are and How They Work

Understanding Enzymes in Biochemical Reactions

This is a restriction enzyme or endonuclease, a type of enzyme that cuts a DNA molecule at a specific location.
This is a restriction enzyme or endonuclease, a type of enzyme that cuts a DNA molecule at a specific location. Callista Images / Getty Images

Definition of an Enzyme

An enzyme is defined as a macromolecule that catalyzes a biochemical reaction. In this type of chemical reaction, the starting molecules are called substrates. The enzyme interacts with a substrate, converting it into a new product. Most enzymes are named by combining the name of the substrate with the -ase suffix (e.g., protease, urease). Nearly all metabolic reactions inside the body rely on enzymes in order to make the reactions proceed quickly enough to be useful.

Chemicals called activators can enhance enzyme activity, while inhibitors decrease enzyme activity. The study of enzymes is termed enzymology.

There are six broad categories used to classify enzymes:

  1. oxidoreductases - involved in electron transfer
  2. hydrolases - cleave the substrate by hydrolysis (uptaking a water molecule)
  3. isomerases - transfer a group in a molecule to form an isomer
  4. ligases (or synthetases) - couple the breakdown of a pyrophosphate bond in a nucleotide to the formation of new chemical bonds
  5. oxidoreductases - act in electron transfer
  6. transferases - transfer a chemical group from one molecule to another

How Enzymes Work

Enzymes work by lowering the activation energy needed to make a chemical reaction occur. Like other catalysts, enzymes change the equilibrium of a reaction, but they aren't consumed in the process. While most catalysts can act on a number of different types of reactions, a key feature of an enzyme is that it is specific.

In other words, an enzyme that catalyzes one reaction won't have any effect on a different reaction.

Most enzymes are globular proteins that are much larger than the substrate with which they interact. They range in size from 62 amino acids to more than 2,500 amino acid residues, but only a portion of their structure is involved in catalysis.

The enzyme has what is called an active site, which contains one or more binding sites that orient the substrate in the correct configuration and also a catalytic site, which is the part of the molecule that lowers activation energy. The remainder of an enzyme's structure acts primarily to present the active site to the substrate in the best way. There may also be allosteric site, where an activator or inhibitor can bind to cause a conformation change that affects the enzyme activity.

Some enzymes require an additional chemical, called a cofactor, for catalysis to occur. The cofactor could be a metal ion or an organic molecule, such as a vitamin. Cofactors may bind loosely or tightly to enzymes. Tightly-bound cofactors are called prosthetic groups.

Two explanations of how enzymes interact with substrates are the "lock and key" model, proposed by Emil Fischer in 1894, and the induced fit model, which is a modification of the lock and key model that was proposed by Daniel Koshland in 1958. In the lock and key model, the enzyme and the substrate have three-dimensional shapes that fit each other. The induced fit model proposes enzyme molecules can change their shape, depending on the interaction with the substrate.

In this model, the enzyme and sometimes the substrate change shape as they interact until the active site is fully bound.

 

Examples of Enzymes

Over 5,000 biochemical reactions are known to be catalyzed by enzymes. The molecules are also used in industry and household products. Enzymes are used to brew beer and to make wine and cheese. Enzyme deficiencies are associated with some diseases, such as phenylketonuria and albinism. Here are a few examples of common enzymes:

  • Amylase in saliva catalyzes the initial digestion of carbohydrates in food.
  • Papain is a common enzyme found in meat tenderizer, where it acts to break the bonds holding protein molecules together.
  • Enzymes are found in laundry detergent and stain removers to help break up protein stains and dissolve oils on fabrics.
  • DNA polymerase catalyzes a reaction when DNA is being copied and then checks to make sure the correct bases are being used.

    Are All Enzymes Proteins?

    Nearly all known enzymes are proteins. At one time, it was believed all enzymes were proteins, but certain nucleic acids, called catalytic RNAs or ribozymes, have been discovered that have catalytic properties. Most of the time students study enzymes, they are really studying protein-based enzymes, since very little is known about how RNA can act as a catalyst.

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    Helmenstine, Anne Marie, Ph.D. "Enzyme Biochemistry - What Enzymes Are and How They Work." ThoughtCo, May. 3, 2016, thoughtco.com/enzyme-biochemistry-4042435. Helmenstine, Anne Marie, Ph.D. (2016, May 3). Enzyme Biochemistry - What Enzymes Are and How They Work. Retrieved from https://www.thoughtco.com/enzyme-biochemistry-4042435 Helmenstine, Anne Marie, Ph.D. "Enzyme Biochemistry - What Enzymes Are and How They Work." ThoughtCo. https://www.thoughtco.com/enzyme-biochemistry-4042435 (accessed November 19, 2017).