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Enzymes Overview

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Enzymes Overview

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Overview

enzyme characteristics

  • Increase rate of reaction by lowering activation energy
  • Most are proteins
  • Specific – conversion of one specific substance to one product
  • May require cofactors or coenzymes
  • Carefully regulated

ΔG = free energy

  • Free energy of the product minus the free energy of the reactants
  • ΔG is negative for enzymatic reaction because energy is released (exergonic reaction)

ΔEa = activation energy

  • Energy barrier that must be overcome for a reaction to proceed
  • Enzymes lower activation energy of a reaction by stabilizing transition state
  • Energy required to get to equilibrium (rate of forward and reverse reactions are the same) correlates with ΔG and is unchanged in the presence or absence of enzyme
  • Enzyme doesn't dictate whether reaction will proceed but determines speed of reaction

ENZYME ACTIVE SITE

  • 3D structure produces active site
  • Shaped so that substrate fits in
  • Product of an enzymatic reaction has lower affinity for binding site: exits binding site and is released

COFACTORS AND COENZYMES

  • Bind cofactor binding site (distinct from active site)
  • Some enzymes inactive without cofactor or coenzyme
  • Many are vitamin-derived, metal ions, or other smaller organic molecules

Full-Length Text

  • Here we will learn about the general properties of enzymes: biological catalysts which are essential to many physiological reactions in the body.
  • Start a table so that we can denote some key features of enzymes.
  • Denote that enzymes are biological catalysts that increase the rate of reaction by lowering activation energy.
  • Denote that enzymes catalyze the conversion of a substance called a substrate, to another substance, called a product.
    • Enzymes act on a substrate to speed up the rate of creation of the product.
  • Denote that most enzymes are proteins, although RNA enzymes also exist.
    • This means that the same physiological conditions that affect proteins also affect enzymes.
  • Denote that enzymes are specific: any given enzyme will catalyze the conversion of a specific substrate to a specific product.
  • Denote that enzymes may require other organic or inorganic molecules, called coenzymes or cofactors, to enhance their activity.
  • Denote that enzyme activity is carefully regulated within the cell to control the rates of enzyme-catalyzed reactions.

Let's start by drawing an energy diagram for an enzyme catalyzed reaction, to show how enzymes increase the rate of reaction.

  • Draw a pair of axes.
  • Label the x axis "Reaction Progress".
  • Label the y axis "Free energy".
  • Label the free energy of the substrate near the middle of the y axis.
  • Label the free energy of the product near the bottom of the y axis.
    • This shows their free energy in a given reaction.
  • Dash a horizontal line from substrate.
  • Then, dash horizontal line from product.
  • To indicate the change in free energy when a reaction goes from substrate to product, label the distance between "substrate" and "product" as delta-G, which, as we've learned elsewhere is negative in a spontaneous reaction.
  • We calculate delta G as the free energy of the product minus the free energy of the reactants, thus delta G is a negative value for a spontaneous reaction, which is also an exergonic reaction, because energy is released.
  • Now draw a line with a hump in it to show the reaction progress from substrate to product.
  • Label the distance between the substrate and the top of the hump as "delta-E-A", the activation energy of the reaction, with no enzyme present.
  • Indicate that activation energy is the energy barrier that must be overcome for a reaction to proceed.
  • Now draw another line with a smaller hump to show the reaction progress from substrate to product in the presence of an enzyme.
  • Label the distance between the substrate and the top of the second hump as "delta-E-A-e", the activation energy of the reaction with an enzyme present.
  • Indicate that the energy required to get to equilibrium (the point at which the rate of forward and reverse reactions are the same) correlates with delta G and is unchanged the presence or absence of an enzyme: the enzyme doesn't dictate whether the reaction will proceed but does determine the speed of the reaction.
  • Indicate that enzymes lower the activation energy by stabilizing the transition state between the substrate and the product. We will learn more about this elsewhere.

Now let's depict other key features of enzymes using diagrams.

  • Represent an enzyme as a shape with a space in it, which is the active site of the enzyme.
  • Indicate that enzymes are usually proteins, and that the 3-dimensional structure of the enzyme creates the active site.
    • Recall from elsewhere that parts of the protein that are not close to each other in the primary sequence are brought close together in its 3-dimensional structure.
  • Now redraw our enzyme.
  • Then, to represent different substrates, draw two different shapes next to it: one that is similar to the active-site shape and one that is not.
  • Indicate that the substrate that is shaped like the active site binds to the enzyme.
  • Write that enzymes are specific: they only bind to their particular substrate.
  • Now draw our enzyme bound to its substrate.
  • Write that enzymes speed up the reaction rate, but do not change the reaction equilibrium, as we mentioned before.
  • Finally, draw our enzyme.
  • Then, draw a product that differs in shape from the substrate, which allows the enzyme to release the product, because it has a lower binding affinity.
  • Indicate that enzymes are unchanged by the reaction; they only facilitate the speed of the reaction.

Now let's depict how cofactors affect enzyme activity.

  • Draw another enzyme, but here include two spaces:
    • a larger space to represent the active site
    • a smaller space to represent the cofactor binding site.
  • Write that even though the substrate binds to the active site, the enzyme is not active.
  • Now redraw the enzyme but here show that the cofactor is bound to the cofactor binding site, and the enzyme is active.
  • Write that now that the cofactor is present, the reaction can be catalyzed by the enzyme.
    • Also write that many coenzymes and cofactors are vitamin-derived, metal ions, or other smaller organic molecules.