1. The Biological Catalysts
Enzymes:
The Biological Catalysts

2. Energy of Activation
The energy used to break the bonds in the reactants so they can be reformed in the products is called the energy of activation.
As the hydrogen gas and oxygen gas bonds are broken and new ones are formed the system has a net loss of free energy. In a system, such as the Hindenburg, that energy is released as heat and light. However, unlike the Hindenburg, where a spark provided the energy of activation, the combining of hydrogen and oxygen to make water during cellular respiration cannot rely on heat for the energy of activation. Heat energy would cause molecules such as proteins to decompose.
Cells must rely on catalysts, which are molecules that speed up a chemical reaction without being consumed in the chemical reaction. Most inorganic catalysts provide a surface on which the chemical reaction can take place and thereby lower the amount of activation energy required to a more cell friendly quantity. Organic catalysts come in the form of proteins (or RNA molecules).

3. Enzymes
Enzymes are biological catalysts that increase the reaction rate of biochemical reactions.
Characteristics of enzymes
Made of proteins (or RNA).
They are very specific and only work with a certain set of reactants or substrates that fit on their active site.
Most enzymes are proteins, but recently it had been discovered that certain molecules of RNA can also have enzymatic properties.
Terms
Substrate- These are reactants that interact with the enzyme during a biochemical reaction.
Active site- This is the part of the enzyme actually involved in the chemical reaction.
The enzyme shown is lysozyme

4. Induced Fit Enzymes can be used over and over again.
When an enzyme binds with the substrate, the substrate interacts with the enzyme causing it to change shape. This change in shape facilitates the chemical reaction to occur. This is called the induced fit.

5. Enzyme Example Ribonuclease
Ribonuclease decomposes RNA, and the nucleotides can be recycled.
The purple part is the enzyme; the green part is the substrate (RNA).

6. Enzymes Work by Lowering the Energy of Activation
Enzymes increase the reaction rate by lowering the energy of activation. They do NOT change Gibbs free energy or G.

7. The Enzyme Sucrase Decomposing Sucrose
Note that names of molecules ending in the suffix –ase are enzymes.

8. Effect of Increasing Temperature and Reaction Rates
There are many factors that can affect the reaction rates of enzymes.
Temperature- at first an increase in temperature will increase the reaction rate because of the kinetics of the reaction, but after a certain temperature is reached, the hydrogen bonds fall apart and the enzyme will denature. Notice that with thermophiles natural selection has favored enzymes that can tolerate higher temperatures. For these bacteria, the optimum temperature is 70o C for most of their enzymatic reactions.

9. Effect of Varying pH and Enzymatic Reaction Rates
2. pH can also affect the reaction rates. Most enzymes work best at a range of 6 to 8, but there are some exceptions, such as pepsin. If the environment changes much from the optimum pH, again hydrogen bonds are affected, denaturing the enzyme. Notice that this is more of a bell shaped curve because both an increase and a decrease in pH from the optimum can denature the enzyme. Sometimes the hydrogen bonds that are affected are not at the active site and therefore the enzyme will still work. As the pH moves further from the optimum pH, it increases the likelihood that the active site is disrupted.

10. Effect of Competitive Inhibitors and Enzymatic Reaction Rates
Enzyme inhibitors- Some chemicals inhibit the action of an enzyme.
A competitive inhibitor is a molecule that resembles the substrate enough that it can bind to the active site in place of the substrate. This will slow down the reaction rate as a certain percentage of the enzyme will combine with the inhibitor.

11. Effect of Noncompetitive Inhibitors and Enzymatic Reaction Rates
A noncompetitive inhibitor is one that does not bind to the receptor site but to some other place on the molecule causing a conformational change in the enzyme (protein). This causes the active site to change shape so that substrate cannot bind. This also slows down the reaction rate.

12. Effect of Allosteric Regulation
4. Allosteric Regulation-= regulation by changing the structure of a molecule (allosteric = Greek for “different structure”). Such enzymes have two or more polypeptide chains each with its own active site. This enzyme also has two conformations-one with a functional active site and the other with a nonfunctional active site. This enzyme also has a place for the binding of an activator and an inhibitor. The activator will stabilize the conformation with the functional active site and the inhibitor will stabilize the inactive form of the enzyme.

13. Cooperativity
6. Cooperativity- This occurs when there are two or more sub-units to an enzyme, each with its own active site. When one substrate binds with one active site, the enzyme changes conformation so that the binding of other substrates are easier to achieve.