Chapter Three: Enzymes

Biocatalysts Most Enzymes are Proteins Enzymes with different molecular forms but that catalyze the same reaction called isozymes. Some RNA molecules may act as biocatalysts (called ribozymes) RNA catalyze the formation of peptide bonds between amino acids. Ribosomes are composed of RNA and protein. However, the active part of the ribosome is RNA. This is a rare example of non-protein enzymes.

Examples of enzymes… Catalase catalyzes the decomposition of hydrogen peroxide into water and oxygen. 2H2O2  2H2O + O2 One molecule of catalase can break down 40 million molecules of hydrogen peroxide each second. What is the reaction rate?

Examples of enzymes… Carbonic anhydrase. Found in red blood cells where it catalyzes the reaction: CO2 + H2O H2CO3 It enables red blood cells to transport carbon dioxide from the tissues to the lungs. One molecule of carbonic anhydrase can process one million molecules of CO2 each second.

Enzymatic Reaction Substrates are combined into a larger product Substrate is broken down into smaller products Substrates are combined into a larger product

Enzyme Function In order to do its work, an enzyme must unite - even if ever so briefly - with at least one of the reactants. In most cases, the forces that hold the enzyme and its substrate are noncovalent: - Hydrogen bondings - Ionic interactions - Hydrophobic interactions

Active Site A) The folding of the polypeptide chain typically creates a crevice or cavity on the enzyme surface. This crevice contains a set of amino acid side chains disposed in such a way that they can make noncovalent bonds only with certain ligands. (B) Close-up view of an actual binding site showing the hydrogen bonds and ionic interactions formed between an enzyme and its ligand

Active Site

Specificity The requirement for complementarity in the configuration of substrate and enzyme explains the remarkable specificity of most enzymes. Generally, a given enzyme is able to catalyze only a single chemical reaction or, at most, a few reactions involving substrates sharing the same general structure. However, some enzymes are not specific and can catalyze varieties of substrates.

How Enzymes Work

Co-Factors Many enzymes require the presence of an additional, nonprotein, cofactor. Some of these are metal ions such as Zn2+ (the cofactor for carbonic anhydrase), Cu2+, Mn2+, K+, and Na+. Some cofactors are small organic molecules called coenzymes. Biocytin, lipoamide, flavin mononucleotide, etc. are examples of coenzymes. Biocytin Lipoamide Flavin mononucleotide

Coenzymes may be covalently bound to the protein part (called the apoenzyme) of enzymes as a prosthetic group. Others bind more loosely and, in fact, may bind only transiently to the enzyme as it performs its catalytic act.

Enzyme Naming Trivial name Gives no idea of source, function or reaction catalyzed by the enzyme. Example: trypsin, thrombin, pepsin.

Systematic Name According to the International Union Of Biochemistry (I. U. B.) an enzyme name has two parts: - First part is the name of the substrates for the enzyme. - Second part is the type of reaction catalyzed by the enzyme. This part ends with the suffix “ase”. Example: Lactate dehydrogenase

EC number Enzymes are classified into six different groups according to the reaction being catalyzed. The nomenclature was determined by the Enzyme Commission in 1961 (with the latest update having occurred in 1992), hence all enzymes are assigned an “EC” number. The classification does not take into account amino acid sequence, protein structure, or chemical mechanism.

EC numbers EC numbers are four digits, for example a.b.c.d, where “a” is the class, “b” is the subclass, “c” is the sub-subclass, and “d” is the sub-sub-subclass. The “b” and “c” digits describe the reaction, while the “d” digit is used to distinguish between different enzymes of the same function based on the actual substrate in the reaction. Example: EC number alcohol oxidoreductase is 1.1.1.1

The Six Classes EC 1. Oxidoreductases EC 2. Transferases EC 3. Hydrolases EC 4. Lyases EC 5. Isomerases EC 6. Ligases More information on these classes and their sub-classes can be accessed through the following link: http://www.chem.qmul.ac.uk/iubmb/enzyme/index.html

EC 1. Oxidoreductases EC 1. Oxidoreductases :catalyze the transfer of hydrogen or oxygen atoms or electrons from one substrate to another, also called oxidases, dehydrogenases, or reductases. Note that since these are ‘redox’ reactions, an electron donor/acceptor is also required to complete the reaction.

EC 2. Transferases EC 2. Transferases – catalyze group transfer reactions, excluding oxidoreductases (which transfer hydrogen or oxygen and are EC 1). These are of the general form: A-X + B ↔ BX + A

EC 3. Hydrolases EC 3. Hydrolases – catalyze hydrolytic reactions. Includes lipases, esterases, nitrilases, peptidases/proteases. These are of the general form: A-X + H2O ↔ X-OH + HA

EC 4. Lyases EC 4. Lyases – catalyze non-hydrolytic (covered in EC 3) removal of functional groups from substrates, often creating a double bond in the product; or the reverse reaction, i.e., addition of functional groups across a double bond. A-B → A=B + X-Y X Y Includes decarboxylases and aldolases in the removal direction, and synthases in the addition direction.

EC 5. Isomerases EC 5. Isomerases – catalyzes isomerization reactions, including racemizations and cis-tran isomerizations.

EC 6. Ligases EC 6. Ligases - catalyzes the synthesis of various (mostly C-X) bonds, coupled with the breakdown of energy-containing substrates, usually ATP