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Just as there is a shorthand to represent atoms and molecules in the cell, there is also a shorthand for drawing reactions. Chemical equations diagram the conversion of molecules from one structure to another (Figure 2.11). An equation will show two sets of chemical or structural formulas separated by an arrow indicating the direction of the reaction. Typically, on the left side will be the reactants and on the right side will be the products. The arrow between the two can point only one way or it can be double sided, indicating a reversible reaction. Actually, most reactions can proceed in both forward and reverse directions. If neither the reactants nor the products are removed from the system, the reaction will proceed toward an equilibrium, at which point the forward and reverse reactions will occur at the same rate. Chemical equations must be balanced, containing the same number and types of atoms on each side of the reaction.
As an example of a chemical reaction, consider what happens when you put oxygen gas and hydrogen gas together in a container and light a match, an explosion will take place forming water. This reaction is reversible, if water is placed in a test tube and an electric current is applied, hydrogen and oxygen gas will bubble up from the solution.
Figure 2.11. A simple chemical equation. The conversion of hydrogen gas and oxygen to water. Note that the reverse is also possible.
Organisms basically take energy and use it to rearrange chemicals with the ultimate goal of producing more of themselves. There are thousands of chemical reactions in a cell. To get each of these needed chemical rearrangements to take place the total reaction has to be favorable, resulting in the release of free energy that can be captured for later or used to drive the construction of something. No reaction in the cell will take place if it isn't favorable. In the case of food digestion, these reactions are naturally favorable and they net the organism extra energy. When something is being built, like a protein or cell wall, the reactions by themselves are not favorable. The cell drives these along by linking them with the release of chemical energy, often in the form of the breakdown of high-energy phosphate compounds. The breakdown of the phosphate compound in these reactions is dependent upon the building of the desired product. Since more energy is gained in releasing the phosphate than is used up to make the product, the reaction becomes favorable.
The concentration of substrates and products also has a tremendous influence on the rate of any reaction. A large amount of substrate will increase the rate of a reaction and a large amount of product can inhibit it. This has two implications for the cell. First, substrates have to be of a high enough concentration so that the reactions can occur. Since compounds in the environment are typically at low concentration, the cell must accumulate them against that concentration gradient. Second, the cell sometimes pulls reactions along by immediately removing product. This is especially true for reactions that are reversible and result in similar concentrations of substrates and products.
A common theme of many of the reactions in the cell is the shuttling of electrons from one molecule to another. The biosynthesis of many cell components and the generation of energy in a majority of microbes involves electrons changing molecular hands. These are termed oxidation-reduction reactions or redox reactions and many students of microbiology have a difficult time understanding how they work. As a first attempt, that will oft be repeated to make sure you get the point, we will now expose them at their most intimate level. In a redox reaction, electrons pass from one molecule, which is oxidized, to a second molecule, which is reduced. As an example lets look at one of the steps of glycolysis, a digestive pathway that you have in your cells. (Figure 2.12)
Figure 2.12. Oxidation of glyceraldehyde 3-phosphate to 1,3 bisphophoglycerate. Note the removal of electrons from the carbon molecule and their addition to NAD Electrons are removed from the highlighted carbon and donated to NAD+.
Glyceraldehyde has an aldehyde group associated with its first carbon. This aldehyde carbon is attached to one carbon, one oxygen and one hydrogen. It shares a total of 4 electrons, one with carbon, one with hydrogen and two with oxygen. During the reaction, the hydrogen and its electron are pulled off of glyceradehyde-3-phosphate and given to the NAD molecule. This leaves carbon with an unfilled orbital and it reacts with a nearby phosphate to satisfy that need, forming 1,3 bisphosphoglycerate. In this reaction glyceradehyde is oxidized, it loses electrons and NAD is reduced, it gains electrons. We will discuss these ideas in more detail in the chapter on metabolism.
This ends our review of basic chemistry. We now move on to consider these chemical concepts in the context of biological molecules. In this chapter we will review the common monomers and simple polymers that make up the cell: sugars, nucleic acids, proteins and lipids. In Chapter 3 we will examine how these building blocks are put together to make the structures of the bacterial cell.
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