Enzymes

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This plot shows that a catalyst decreases the activation energy for a reaction but does not change the Gibbs free energy.
Enzymes lower the reaction’s activation energy but do not change the reaction’s free energy.

Source: OpenStax Biology 2e

OpenStax Biology 2e

A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are enzymes. Almost all enzymes are proteins, comprised of amino acid chains, and they perform the critical task of lowering the activation energies of chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily. It is important to remember that enzymes do not change the reaction’s ∆G. In other words, they do not change whether a reaction is exergonic (spontaneous) or endergonic. This is because they do not change the reactants’ or products’ free energy. They only reduce the activation energy required to reach the transition state.

– What are proteins that have sequence homology with enzyme families but are proven or predicted to lack enzyme activity due to mutations in otherwise conserved catalytic amino acids?

Enzyme Active Site and Substrate Specificity

The chemical reactants to which an enzyme binds are the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate breaks down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is the enzyme’s active site. This is where the “action” happens. Since enzymes are proteins, there is a unique combination of amino acid residues (also side chains, or R groups) within the active site. Different properties characterize each residue. These can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of amino acid residues, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind, albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), enzymes are known for their specificity. The “best fit” results from the shape and the amino acid functional group’s attraction to the substrate. There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is flexibility as well.

– What interacts with an enzyme and decreases the enzyme’s catalytic efficiency?

The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to local enviromental influences. It is true that increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, a process that changes the substance’s natural properties. Likewise, the local environment’s pH can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties that are optimal for catalysis. These residues are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature.

– What is the location on the enzyme surface where substrates bind, and where the chemical reaction catalyzed by the enzyme occurs?

Enzyme activity is usually the objective of growing bugs in a plant. Enzymes are biological catalysts. Just like other catalysts, they reduce activation energy, allowing reactions to proceed in a desired direction. Because their activity is dependent on the folding of a protein, they are usually sensitive to the temperature, pH, and salt concentration of the environment they work in. Thus, pH, salt, and temperature are effective in preserving foods. There are exceptions to this, such as the enzymes put in washing powder, which come from bacteria evolved to survive in hot springs, but the general rule is that small deviations from their tolerable ranges can reduce activity. Larger excursions may denature them irreversibly.

Source:

Clark, M., Douglas, M., Choi, J. Biology 2e. Houston, Texas: OpenStax. Access for free at: https://openstax.org/details/books/biology-2e

https://stke.sciencemag.org/content/12/594/eaat9797

https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Map%3A_Physical_Chemistry_for_the_Biosciences_(Chang)/10%3A_Enzyme_Kinetics/10.5%3A_Enzyme_Inhibition

http://www.biology.arizona.edu/biochemistry/problem_sets/energy_enzymes_catalysis/01t.html

https://www.sciencedirect.com/book/9780128113097/an-applied-guide-to-water-and-effluent-treatment-plant-design


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