Bis2A: 2.3 Interpreting Chemical Reactions

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1 OpenStax-CNX module: m Bis2A: 2.3 Interpreting Chemical Reactions The BIS2A Team This work is produced by OpenStax-CNX and licensed under the Creative Commons Attribution License 4.0 Abstract This module will discuss the overall methods to reading and interpreting chemical reactions. The main goal for this section is to draw connections between energy, electronegativity, functional groups and the synthesis or degradation of macromolecules and other compounds in the cell. Section Summary Chemical reactions are molecular transformations that begin with reactants and end with products. Almost all biological transformation that take place in a cell involve chemical reactions between various small molecules and some of the major categories of macromolecules found in the cell; proteins, carbohydrates, nucleic acids, and lipids. Understanding the basis for the assembly and disassembly of biomolecules is therefore key to developing a functional knowledge of biological processes. 1 Characteristics of Chemical Reactions All chemical reactions begin with a reactant, the general term for the one or more substances that enter into the reaction. Sodium and chloride ions, for example, are the reactants in the production of table salt. The one or more substances produced by a chemical reaction are called the product. **Note that there is some "hidden" excitement in the story about table salt involving water that we'll see soon.** In chemical reactions, the atoms and elements present in the reactant(s) must all also be present in the product(s). Similarly, there can be nothing present in the products that was not present in the reactants. This is because chemical reactions are governed by the law of conservation of mass, which states that matter cannot be created or destroyed in a chemical reaction. This means when you examine a chemical reaction you must try to account for everything that goes in AND make sure you can nd it all in the stu the comes out! Just as you can express mathematical calculations in equations such as = 9, you can use chemical equations to show how reactants become products. By convention, chemical equations are typically read or written from left to right. Reactants on the left are separated form products on the right by an single or double-headed arrow indicating the direction in which the chemical reaction proceeds. For example, the chemical reaction in which one atom of nitrogen and three atoms of hydrogen produce ammonia would be written as N + 3H NH 3. Correspondingly, the breakdown of ammonia into its components would be written as NH 3 N + 3H. Version 1.1: Jan 2, :19 pm

2 OpenStax-CNX module: m Note that in either direction you nd 1 N and 3 Hs on both sides of the equation. Reversability In theory, any chemical reaction can proceed in either direction under the right conditions. Reactants may synthesize into a product that is later revert back to a reactant. Reversibility is also a quality of exchange reactions. For instance, A + BC AB + C could then reverse to AB + C A + BC. This reversibility of a chemical reaction is indicated with a double arrow: A + BC[U+21C4]AB + C. So, if reactants become products that can revert to the reactant form how do you know what is a reactant and what is a product? It's a bit confusing. FILL IN HERE Synthesis Reactions Many macromolecules are made from smaller subunits, or building blocks, called monomers. Monomers covalently link to form larger molecules known as polymers. Often the synthesis of polymers from monomers will also produce water molecules as products of the reaction. This type of reaction is known as dehydration synthesis or condensation reaction. Figure 1: In the dehydration synthesis reaction depicted above, two molecules of glucose are linked together to form the disaccharide maltose. In the process, a water molecule is formed. note: Try to complete the parts of an Energy Story for the reaction above that have to do with the accounting of mass. We will begin learning how to ll in the energy and mechanism components later. See if together you can craft statements that are both accurate and concise. In a dehydration synthesis reaction (Figure 1), the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water. At the same time, the monomers share electrons and form covalent bonds. As additional monomers join, this chain of repeating monomers forms a polymer. Dierent types of monomers can combine in many congurations, giving rise to a diverse group of macromolecules. Even one kind of monomer can combine in a variety of ways to form several dierent polymers: for example, glucose monomers are the constituents of starch, glycogen, and cellulose. In the carbohydrate monomer example above the polymer is formed by a dehydration reaction, this type of reaction is also used to add amino acids to a growing peptide chain, and nucleotides to the growing DNA or RNA polymer. Visit the modules on Amino Acids, Lipids, and Nucleic Acids to see if you can identify the water molecules that are removed when a monomer is added to the growing polymer. Hydrolysis Reactions Polymers are broken down into monomers in a reaction known as hydrolysis. A hydrolysis reaction includes a water molecule as a reactant(figure 2). During these reactions, a polymer can be broken into two components: one product carries a hydrogen atom (H+) from the water while the second product carries the water's remaining hydroxyl group (OH).

3 OpenStax-CNX module: m Figure 2: In the hydrolysis reaction shown here, the disaccharide maltose is broken down to form two glucose monomers with the addition of a water molecule. Note that this reaction is the reverse of the synthesis reaction shown in gure 1 above. Dehydration synthesis and hydrolysis reactions are catalyzed, or sped up, by specic enzymes. Note that both dehydration synthesis and hydrolysis reactions involve the making and breaking of bonds between the reactants - a reorganization of how the atoms in the reactants are bonded together. In biological systems (our bodies included), food in the form of molecular polymers is hydrolyzed into smaller molecules by water and enzymes in the digestive system. This allows for the smaller nutrients to be absorbed and reused for a variety of purposes. In the cell, monomers derived from food may then be reassembled into larger polymers that serve new functions. For Additional Information: Visit this site 1 to see visual representations of dehydration synthesis and hydrolysis. Example of Hydrolysis with Enzyme Action is shown in this 3 minute video entitled: hydrolysis of sucrose by sucrase

4 OpenStax-CNX module: m The Three Fundamental Chemical Reactions Figure 3: The atoms and molecules involved in the three fundamental chemical reactions can be imagined as words. A synthesis reaction (a) is a chemical reaction that results in the synthesis (joining) of components that were formerly separate. A hydrolysis reaction (b) is a chemical reaction that breaks down or lyses something larger into its constituent parts. An exchange reaction (c) in which both synthesis and hydrolysis can occur, chemical bonds are both formed and broken, and energy is redistributed. The gure above represents a synthesis reaction (a), a hydrolysis reaction (b) and a third type of reaction, an exchange reaction (c). An exchange reaction is a chemical reaction in which both synthesis and hydrolysis can occur, chemical bonds are both formed and broken, and chemical energy is absorbed, stored, and released. The simplest form of an exchange reaction might be: A + BC AB + C. Notice that, to produce these products, B and C had to break apart in a decomposition reaction, whereas A and B had to bond in a synthesis reaction. A more complex exchange reaction might be:ab + CD AC + BD. Another example might be: AB + CD AD + BC. 2 Review Questions Exercise 1 (Solution on p. 7.) What role do electrons play in dehydration synthesis and hydrolysis? 3 Energy in Chemical Reactions Chemical reactions typically involve a redistribution of energy within the chemical reactants and products and with their environment. So, like it or not, we need to develop some models that can describe where energy is in a system (perhaps how it is stored) and how it can be moved around sets of molecules. The models we develop will not be overly detailed - in the sense that they would satisfy a hard-core chemist or physicist with technical detail - but we expect that they should still be technically correct and help to not start forming incorrect mental models that will make getting the "renements" down later. In this respect, one of the key concepts to understand is that we are going to view energy as something that is transferred

5 OpenStax-CNX module: m between things in a system. It is NOT transformed into dierent things. Transfer vs. transform - that's important. The latter gives the impression that energy is something which exists in dierent forms, that it gets reshaped somehow. No. It's hard to deal with something that is being conserved in a process if it constantly changing form. Those two ideas are inconsistent. So, we are going to transfer energy between dierent things instead and that it can be stored dierent places. That'll hopefully make the accounting easier. Since we are will often be dealing with transformations of biomolecules we can start by thinking about where energy can be found/stored in these systems. We'll start with a couple of ideas and add more to them later. Let us propose that one place that energy can be stored is in the motion of matter. For brevity we'll give the energy stored in motion a name: kinetic energy. Molecules in biology are in constant motion and therefore have a certain amount of kinetic energy (energy stored in motion) associated with them. Let us also propose that there is a certain amount of energy stored in the biomolecules themselves and that the amount of energy stored in those molecules is associated with the types and numbers of atoms in the molecules and the their organization (the number and types of bonds between them). The discussion of exactly where the energy is stored in the molecules is beyond the scope of this class but we can approximate it by suggesting that a good proxy is in the bonds. Dierent types of bonds may be associated with storing dierent amounts of energy. In some contexts this type of energy storage could be labeled potential energy or chemical energy. With this view, one of the things that happens during the making and breaking of bonds in a chemical reaction is that the energy is transferred about the system into dierent types of bonds. In the context of an Energy Story one could theoretically count the amount of energy stored in the bonds and motion of the reactants and the energy stored in the bonds and energy of the products. In some cases you might nd that when you add up the energy stored in the products and the energy stored in the reactants that these sums are not equal. If the energy in the reactants is greater than the products where did this energy go? It had to get transferred to something else. Some will certainly have moved into other parts of the system stored in the motion of other molecules (warming the environment) or perhaps in the energy associated with photons of light. One good real life example is the chemical reaction between wood and oxygen in the air and it's conversion to carbon dioxide and water. At the beginning, the energy in the system is largely in the molecular bonds of oxygen and the wood (reactants). There is still energy left in the carbon dioxide and water (products) but less than at the beginning. We all appreciate that some of that energy was transferred to the energy in light and heat. This reaction where energy is transferred to the environment is termed exothermic. By contrast, in some reactions energy will transfer in from the environment. These reactions are called endothermic. The transfer of energy in or out of the reaction from the environment is NOT the only thing that determines whether a reaction will be spontaneous or not. We'll discuss that soon. For the moment, it is important to get comfortable with the idea that energy can be transferred between dierent components of a system during a reaction and that you should be able to envision tracking it. 4 Enzymes and Catalysts For a chemical reaction to happen the substrates must rst nd one another in space. In fact, in many cases it's more complicated. Not only do the substrates need to run into one another but they need to come into contact in a specic orientation. Since chemicals don't "plan" these collisions need to happen relatively randomly. If reactants are very dilute the rate of the reaction will be slow - collisions will happen infrequently. Increasing the concentrations will increase the rate of productive collisions. Another way to change the rate of reaction is to increase the rate of collisions by increasing the rate at which the reactants explore the reaction space - by increasing the velocity of the molecules or their kinetic energy. This can be accomplished by transferring heat into the system. Those two are sometimes decent strategies for increasing

6 OpenStax-CNX module: m the rates of chemical reactions that happen in a tube. However, in the cell the transfer of heat may not be practical (it may damage cellular components) and lead to death. Cells sometimes use mechanisms to increase concentrations of reactants (we'll see some examples) but this is rarely sucient to drive reaction rates in a biologically relevant regime. That is where catalysts come in. A catalyst is a something that helps increases the rate of a chemical reaction without itself undergoing any change. You can think of a catalyst as a chemical change agent. The most important catalysts in biology are called enzymes. An enzyme is a protein catalyst. Other cellular catalysts include molecules called ribozymes. A ribozyme is a catalyst composed of a ribonucleic acid (RNA). Both of these will be discussed in more detail later in the course. Like all catalysts, enzymes work by lowering the level of energy that needs to be transferred into a chemical reaction to make it happen. A chemical reaction's activation energy is the threshold level of energy needed to initiate the reaction. Figure 4: Enzymes decrease the activation energy required to initiate a given chemical reaction. (a) Without an enzyme, the energy input needed for a reaction to begin is high. (b) With the help of an enzyme, less energy is needed for a reaction to begin. note: Can you create a very basic energy story for the generic reaction above? Practice going through the list of steps. You may need to make up or simplify things - for instance you might need to say that the mass of the reactants at the start is split between two forms and at the end the mass has combined into one form. Make up other ideas that make sense if you need to. note: Look at gure 4. What do you think the units are on the x-axis? Time would be one guess. However, if you compare the gures it appears that the products are formed at the same time whether the activation energy barrier is high or low. Wasn't the point of this gure to illustrate that reactions with high activation energy barriers were slower than those with low activation energy barriers? What's going on?

7 OpenStax-CNX module: m Solutions to Exercises in this Module to Exercise (p. 4) In a dehydration synthesis reaction, the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water. This creates an opening in the outer shells of atoms in the monomers, which can share electrons and form covalent bonds.