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Enzymes- The Biological catalysts

©2000 Timothy Paustian, University of Wisconsin-Madison

Many of the reactions in catabolism are favorable (they have a negative DG). What this means is that these reactions will occur spontaneously even outside of a living organism. The problem is, they are way too slow to be of any use in a biological system! If cells did not have ways of speeding up catabolism, life would be nearly impossible. Enzymes accelerate almost all biological reactions.

Enzyme structure

Enzymes are proteins, which themselves are polymers of amino acids. For more information on Protein Structure see the bacterial structure section. They range in size from 1 x 10⁴ daltons to 1 x 10⁶ daltons with most being in the 10⁵ range. Some enzymes have extra molecules associated with them, besides amino acids, that assist in the reaction they carry out. The protein portion of an enzyme is called the apoenzyme. A cofactor is the non-protein part of an enzyme. Cofacors can be loosely bound, coenzymes or tightly bound, prosthetic groups. The complete enzyme (apoprotein + cofactor) is termed the holoenzyme.

Figure 1 - The potential parts of a typical enzyme. Not every enzyme will have a prosthetic group or a coenzyme. Each enzyme is unique.

• Red blood cells contain the protein hemoglobin which has heme (the oxygen carrier in our blood) as a prosthetic group.

• Many of the vitamins are coenzymes. For example, niacin is a precursor used in the synthesis of NAD⁺ and pantothenic acid is a part of coenzyme A. Vitamins are crucial to catabolism, but they are only needed in trace amounts. Taking them in excess as proposed by some "health experts" usually has no benefit and in some cases can even be harmful.

Enzyme Function

Enzymes convert a target molecule, the enzymes substrate(s), into a different molecule, the enzymes product(s). Enzymatic reactions can have any number of substrates and products, but for this introduction, lets consider a simple case; an enzyme that has two substrates and one product that are joined together.

Figure 2 - An enzymatic reaction with two substrates and one product.

Enzymes are efficient and specific

The efficiency of enzymes is extremely high. They can catalyze the transformation of as many as 10² to 10⁶ molecules per minute. Most also have a high degree of specificity binding a specific molecule and converting it to a specific product. Enzyme and substrate fit into each other like a lock into a key.

Visualizing enzymatic catalysis

To understand how enzymes catalyze reactions, you first have to get you head around the idea of activation energy. Many chemical reactions require an initial amount of energy be added to get them to proceed forward. Even thermodynamically favorable reactions need a little boost of energy. It is helpful to imagine a chemical reaction as a roller coaster ride. To get the ride started you have to roll up an incline, this is the activation energy. Once beyond the top of the incline, the coaster is propelled forward by the force of gravity and no extra energy is needed. The activation energy represents the amount of work that goes into having the substrates come together in a manner that causes the reaction to occur.

Figure 3 - A chemical reaction. To activate the movie, press the "Start" button. Notice how the rate of reaction greatly decreases as the number of substrates decreases.

Enzymes increase the rate of reaction by lowering the activation energy. They lower this activation energy by binding the substrates of the reaction. This causes a reaction to occur for two reasons.

1. Enzymes bind their substrates at what is called the active site. When bound at the active site the substrates are brought into close proximity to one another and will react.

2. The enzyme will bend the substrates in such a manner to make them more reactive. In biochemistry speak, the enzyme binds the substrates in a transition state complex. (Hey, a big word that you can use to make friends and influence people.) This makes it possible for substrates to react and form products.

Figure 4 - A chemical reaction catalyzed by an enzyme. Press the start button to activate the movie. Notice how the simulated enzyme grabs the substrates and holds them together. This speeds up the reaction, especially when the substrates are at low concentrations.

Most enzymes greatly lower the activation energy of their reaction and allow much more substrate to be converted to product per unit time. Every reaction that we will talk about in metabolism is catalyzed by an enzyme, their importance cannot be overstated.

It is becoming clear that bacteria are not little bags of enzymes, but are highly organized. This is reflected in enzyme location. Enzymes are organized by the cell into collections that carry out multi-step conversions. Each enzyme in the collection will take its substrate, convert it to product and hand it off to the next enzyme - analogous to an assembly line. These collections are called biochemical pathways and each is responsible for taking a substrate and converting it into a needed product. Biochemical pathways are classified by their use to the cell and in the next section we will look at different types of catabolic pathways.

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