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Energy Flow and Enzymes

Energy Flow and Enzymes

Enzymes in Detail

Enzymes are basically like the fast-forward button on your DVR remote. While they are buzzing about 24/7 and involving themselves in chemical reactions, they always have these two properties:
  1. They do not change the thermodynamic properties of the reaction
  2. They are not consumed or modified in the reaction.
Enzymes make the reaction go faster, which allows biological reactions to occur on a timescale compatible with Life. Enzymes are like Ricky Bobby: they wanna go fast!

We can also study enzymes in the context of activation energy. Many biochemical reactions need a little input of energy to jump-start a thermodynamically favorable reaction. The activation energy is the amount of energy needed for the reaction to go forward and get over its activation barrier.

ATP (adenosine triphosphate), the cell’s energy carrier, needs a little help to get over its activation barrier. Otherwise, ATP might donate its terminal (read: end) phosphate group prematurely, resulting in an untimely release of energy. That would be bad—very bad. The cell makes sure that a reaction occurs when and where it wants by controlling the availability and abundance of enzymes.

The need to reach the activation energy can be compared to when the Big Thunder Mountain Railroad train needs to be "pulled" up the track and to the top of the little hill before it can go rolling down at exhilarating speeds. Until the train makes it over the little hump, it won’t be able to proceed down the other side. It’s helpful to look at chemical reactions using an energy diagram (see below). Enzymes lower the activation energy of desired reactions and therefore kick-starts them to get them rolling.

Enzymes lower the activation energy of a reaction by binding one of the reactants, called a substrate, and holding it in a way that lowers the activation energy. Say, for instance, that the reaction is the event of hitting a baseball. Your bat needs to come into contact with the ball. One option is for Brian Wilson (The Beard) to show up dressed like that and pitch the ball to you. Good luck hitting the ball when you have such a glorious, uh, beard to look at.

Alternatively, you could play tee ball. Yes, tee ball. Less cool than the previous option, for sure, but now, you are much more likely to actually make your bat meet the ball. Having an enzyme around is a lot like putting a baseball on a tee stand, which increases the chances of a collision between the ball and the bat because it slows the ball down. An enzyme holds its substrate in such a way that the reaction is much more likely to occur.

We mentioned earlier that enzymes are often present in controlled, really small amounts. Amazingly, it is estimated that a typical enzyme will catalyze the reaction of about a thousand substrate molecules every second.1

How efficient an enzyme is at catalyzing a reaction is extremely dependent on the reaction conditions, and especially on how good the enzyme is at finding its substrate. Molecules in the cell are constantly in motion, wandering around the cell in a process called diffusion. In diffusion, molecules move from areas of higher concentration to lower concentration.

You can imagine, though, that the chance that any enzyme will meet its substrate is dependent on how much substrate is in the cell. In this case, the substrate is the limiting factor of the reaction rate, slowing and eventually preventing any further reactions from occurring in its absence. If there is little substrate, the enzyme is less likely to find the substrate and catalyze the reaction.

Alternatively, if the substrate concentration increases and reaches a high amount, the reaction rate becomes dependent on the limiting characteristics of the enzyme. An enzyme is considered to be working at its maximal rate under this condition, where amount of substrate exceeds amount of enzyme. In this way, the cell directly controls the rate of reaction by controlling the amount of enzyme available to the substrate.

Enzymes are usually extremely specific, meaning that one enzyme only catalyzes one type of biochemical reaction. How is the specificity of an enzyme determined? The enzyme has a special site, called the active site, which is a unique binding site that only a particular substrate will recognize and be able to fit inside. The active site is not changed after an enzyme catalyzes a reaction, so a new substrate can still fit in the site when the old substrate has gone away.

Therefore, there are specific enzymes for specific biological reactions. Most biological reactions are also connected, meaning that the product from one enzyme-catalyzed (say, enzyme A) reaction is often used as a reactant in another reaction catalyzed by a different enzyme (say, enzyme B). The result is a complicated network of biochemical reactions.

The different types of enzymes can be divided into groups based on the types of reactions that they catalyze.

The Diversity of Enzymes
Type of EnzymeEnzyme Function
NucleaseCleaves the bond connecting two nucleic acids.
ProteaseCatalyzes the disruption of the bonds that connect amino acids in a protein.
PolymeraseCatalyzes the production of biological polymers, such as RNA and DNA.
KinaseAdds a phosphate to one biological molecule through a process called phosphorylation (very creative). Kinases are important signaling molecules.
ATPaseCatalyzes the conversion of ATP into ADP, which releases energy to drive cellular processes.
PhosphataseCatalyzes the opposite reaction of a kinase by removing a phosphate group
Brain snack

Ever wonder why apples turn brown? Apples brown because of a family of enzymes called PPO (polyphenol oxidase, if you must know) enzymes that catalyze a reaction between the oxygen in the area and the iron-containing compounds in apples. The result? Enzymatic browning.

Own a pair of stonewashed jeans? Think again! Jean manufacturers now use enzymes instead of stones to give jeans the stonewashed look by degrading the denim fabric. This method actually damages the jeans less than the stone method.

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