Enzymes and the Way that They Work

Question: Describe Enzymes and the way that they work. Answer: Structure and function of the enzyme Enzymes are the protein macromolecules. The enzyme possesses three structures namely Primary, Secondary and Tertiary. The amino acids remain interlinked with each other with the help of peptide bonds (primary structure). The NH2 (amino group) and the Oxygen from the COOH (carboxyl group) of the amino acids interact with each other with the help of hydrogen bonding. This interaction leads to -helical and -sheet conformations, which is known as the secondary structure. Furthermore, this secondary structure folds up to form the 3-dimensional tertiary structure which results in the formation of active sites (which binds substrate), allosteric sites in the enzyme. Sometimes inorganic ions like Mg2+, Fe2+, Zn2+ (cofactors) and organic substances (coenzymes remain attached with the enzymes (or apoenzymes) via covalent bonds to form holoenzymes (Cox 2013). Figure 1: A simple structure of an enzyme Source: (Cox 2013) The primary and most important function of an enzyme is to accelerate the rate of a reaction by acting as a biocatalyst. Moreover, the tertiary structure had provided the enzyme with an active/catalytic site. This active site of the enzyme binds specifically with a substrate to produce a final product. For example, enzyme Lipase binds to its specific lipid substrate to form glycerol and fatty acids as products (Berg, Stryer and Tymoczko 2015). Figure 2: Image showing the function of the enzyme that includes the substrate binding and product formation Source: (Berg, Stryer and Tymoczko 2015) Concept of activation energy In a biochemical process, the amount of energy required to start a reaction is known as the activation energy, and it is symbolized as à Ã‚ ªG. Moreover, it is a scientifically proven fact that both reactants (substrate) and products possess a particular energy (Armstrong and Hirst 2015). The transformation of a substrate to product requires a transition phase that has a higher energy value (activation energy). In other words, the substrate requires a higher energy to activate its transformation process to produce its final products. On the other hand, the enzyme lowers this activation energy resulting in a faster reaction rate (Cox 2013). Figure 3: The figure shows the activation energy required to transform a substrate to a product with and without an enzyme Source: (Cox 2013) Lock and key and Induced fit models of enzyme action Lock and key model In 1894, Fischer compared the activity of enzyme and substrate with lock and key. One enzyme can act only on a particular type of substrate just as a key fits a particular lock. Each enzyme possesses a specific part (active site), to which the specific part of the substrate is joined. Biochemical reactions occur in the active site where the enzyme-substrate complex is formed by forming bonds within it (Berg, Stryer and Tymoczko 2015). The bond loosens when the chemical reaction is over, and the product is formed, and the enzyme gets free (Gspri, Vrna, Szappanos and Perczel 2010). Figure 4: The lock and key model of enzyme-substrate interaction Source: (Gspri, Vrna, Szappanos and Perczel 2010) Induced fit theory The induced fit theory is the modernized version of Lock and Key Model. According to this model, as the substrate gets closer, the active site of the enzyme tends to change its shape and conformation. Moreover, scientists have found that the change in the structure of the active site of the enzyme is induced' by the approaching substrate molecule. This change in shape of the active site of the enzyme helps the substrate to easily fit' into the active site of the enzyme. This model of enzyme-substrate interaction is known as the induced fit theory. Moreover, it should be noted that only a specific substrate for a specific enzyme can only bring this conformational change in the active site of the enzyme (Csermely, Palotai and Nussinov 2010). Figure 5: Schematic diagram showing the concept of Induced fit theory Source: (Csermely, Palotai and Nussinov 2010) Effects of three external factors on enzyme The effects of three external factors (Temperature, pH and Enzyme and Substrate concentration) influences the property and functioning of an Enzyme. A detailed discussion is as follows - Temperature: The increase in temperature increases the vibrational energy that significantly affects the bonds present inside enzyme making it weaker. Moreover, it also results in the breakdown of the weaker bonds like hydrogen and ionic bonds inside the enzyme resulting in denaturation of the enzyme (Cox 2013). pH: The H+ and OH- ions interact with the hydrogen and ionic bonds of the enzyme by repelling or attracting them towards itself. This interference results in the change of conformation of the active site of the enzyme that ultimately leads to the impairment of the enzymatic activity (Leu and Zhu 2013). Enzyme and Substrate Concentration: Increase in Enzyme will give rise to an increased rate of reactions. This is because the fact that more enzymes will collide with the substrate resulting in a faster reaction. On the other hand, an increase in the substrate concentration will lead to a similar result as well. As a consequence of an increase in the substrate concentration, more substrate will collide and interact with the enzyme molecule which will produce a higher number of products (Berg, Stryer and Tymoczko 2015). Reference Armstrong, F.A. and Hirst, J., 2011. Reversibility and efficiency in electrocatalytic energy conversion and lessons from enzymes.Proceedings of the National Academy of Sciences,108(34), pp.14049-14054. Berg, J.M., Stryer, L. and Tymoczko, J.L., 2015.Stryer Biochemie. Springer-Verlag. Cox, M.M., 2013.Lehninger principles of biochemistry. Freeman. Csermely, P., Palotai, R. and Nussinov, R., 2010. Induced fit, conformational selection and independent dynamic segments: an extended view of binding events.Trends in biochemical sciences,35(10), pp.539-546. Gspri, Z., Vrnai, P., Szappanos, B. and Perczel, A., 2010. Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action.FEBS letters,584(1), pp.203-206. Leu, S.Y. and Zhu, J.Y., 2013. Substrate-related factors affecting enzymatic saccharification of lignocelluloses: our recent understanding.Bioenergy Research,6(2), pp.405-415.