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CH103 – Chapter 7: Chemical Reactions in Biological Systems

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7.1 What is Metabolism?

7.2 Common Types of Biological Reactions

7.3 Oxidation and Reduction Reactions and the Production of ATP

7.4 Reaction Spontaneity

7.5 Enzyme-Mediated Reactions

7.6 Introduction to Pharmacology

7.7 Chapter Summary

7.8 References

7.1 What is Metabolism?

Metabolism is the set of life-sustaining chemical reactions in organisms. We have seen examples of metabolic processes in the primary and secondary metabolites covered in Chapter 6. Overall, the three main purposes of metabolism are: (1) the conversion of food to energy to run cellular processes; (2) the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and carbohydrates; and (3) the elimination of waste products. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. (The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediate metabolism.)

Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of proteins into amino acids during digestion); or anabolic – the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.

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Figure 7.1 Catabolic and Anabolic Reactions. Catabolic reactions involve the breakdown of molecules into smaller components, whereas anabolic reactions build larger molecules from smaller molecules. Catabolic reactions usually release energy whereas anabolic processes usually require energy.

Figure is modified from Metabolism Overview

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because enzymes act as catalysts – they allow a reaction to proceed more rapidly. In addition, enzymes can provide a mechanism for cells to regulate the rate of a metabolic reaction in response to changes in the cell’s environment or to signals from other cells, through the activation or inhibition of the enzymes activity. Enzymes can also allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzyme shape is critical to the function of the enzyme as it determines the specific binding of a reactant. This can occur by a lock and key model where the reactant is the exact shape of the enzyme binding site, or by an induced fit model, where the contact of the reactant with the protein causes the shape of the protein to change in order to bind to the reactant.

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Figure 7.2 Mechanisms of Enzyme-Substrate Binding. (A) In the Lock and Key Model, substrates fit into the active site of the enzyme with no further modifications to the enzyme shape required. (B) In the Induced Fit Model, substrate interaction with the enzyme causes the shape of the enzyme to change to better fit the substrate and mediate the chemical reaction.

Figure 7.2A was modified from Socratic and Figure 7.2B was modified from Concepts in Biology

7.2 Common Types of Biological Reactions

Within biological systems there are six major classes of biochemical reactions that are mediated by enzymes. These include group transfer reactions, the formation/removal of carbon-carbon double bonds, isomerization reactions, ligation reactions, hydrolysis reactions, and oxidation-reduction reactions. This section will give you a brief introduction to these six types of reactions and then the following section will focus more in-depth on oxidation-reductions and how they are critical for the formation of the major form of cellular energy, adenosine triphosphate (ATP). Note that all of these reaction types require an enzyme catalyst (usually a specific protein) to speed up the rate of the reactions within biological systems.

Group Transfer Reactions

In group transfer reactions, a functional group will be transferred from one molecule that serves as the donor molecule to another molecule that will be the acceptor molecule. The transfer of an amine functional group from one molecule to another is common example of this type of reaction and is shown in Figure 7.3 below.

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Figure 7.3 Transfer of an Amine Functional Group. A common group transfer reaction in biological systems is one that is used to produce α-amino acids that can then be used for protein synthesis. In this reaction, one α-amino acid serves as the donor molecule and an α-keto acid (these molecules contain a carboxylic acid functional group and a ketone functional group separated by one α-carbon) serves as the acceptor. In the acceptor molecule, the carbonyl oxygen is replaced with the amine functional group, whereas in the donor molecule, the amine functional group is replaced by an oxygen forming a new ketone functional group.

The Formation/Removal of Carbon-Carbon Double Bonds

Reactions that mediate the formation and removal of carbon-carbon double bonds are also common in biological systems and are catalyzed by a class of enzymes called lyases. The formation or removal of carbon-carbon double bonds is also used in synthetic organic chemistry reactions to create desired organic molecules. One of these types of reactions is called a hydrogenation reaction, where a molecule of hydrogen (H2) is added across a C-C double bond, reducing it to a C-C single bond. If this is done using unsaturated oils, the unsaturated fats can be converted into saturated fats (Figure 7.4). This type of reaction is commonly done to produce partially hydrogenated oils converting them from liquids at room temperature into solids. Margarines made from vegetable oil are made in this manner. Unfortunately, a by-product of this reaction can be the formation of TAGS containing trans double bonds. Once the health hazards of consuming trans fats was recognized, the Food and Drug Administration (FDA) placed a ban on the inclusion of trans fats in food products. This ban was enacted in the summer of 2015 and gave food-makers three years to eliminate them from the food supply, with a deadline of June 18, 2018.

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Figure 7.4 Hydrogenation of Oils to Produce Margarine. Unsaturated oils can by partially or fully hydrogenated to produce the saturated fatty acids to produce margarines that will remain solid at room temperature. The addition of the new hydrogen atoms to create the saturated hydrocarbons are shown in yellow in the final product.

Upper photo provided by Cottonseed Oil and lower photo provided by Littlegun

Isomerization Reactions

In isomerization reactions a single molecule is rearranged such that it retains the same molecular formula but now has a different bonding order of the atoms forming a structural or stereoisomer. The conversion of glucose 6-phosphate to fructose 6-phosphate is a good example of an isomerization reaction and is shown in figure 7.5

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Figure 7.5 Isomerization of Glucose 6-phosphate to Fructose 6-phosphate.

Ligation Reactions

Ligation reactions use the energy of ATP to join two molecules together. An example of this kind of reaction is the joining of the amino acid with the transfer RNA (tRNA) molecule during protein synthesis. During protein synthesis the tRNA molecules bring each of the amino acids to the ribosome where they can be incorporated into the newly growing protein sequence. To do this, the tRNA molecules must first be attached to the appropriate amino acid. Specific enzymes are available called amino acyl – tRNA synthetases that mediate this reaction. The synthetase enzymes use the energy of ATP to covalently attach the amino acid to the tRNA molecule. A diagram of this process is shown in Figure 7.6. For each of the 20 amino acids, there is a specific tRNA molecule and a specific synthetase enzyme that will ensure the correct attachment of the correct amino acid with its tRNA molecule.

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Figure 7.6 Ligation Reaction Covalently Attaching Methionine with the Appropriate tRNA. The amino-acyl tRNA synthetase enzyme for methionine (shown in blue) covalently attaches methionine (light pink) with the methionine tRNA molecule (dark pink). This reaction requires the energy provided from the breakdown of the ATP molecule into AMP, releasing energy with the breakdown of the phosphate bonds into two inorganic phosphate ions (2 Pi).

Figure provided by the Kahn Academy

Hydrolysis Reactions

The classification of hydrolysis reactions include both the forward reactions that involve the addition of water to a molecule to break it apart or the reverse reaction involving the removal of water to join molecules together, termed dehydration synthesis (or condensation) (Figure 7.7). When water is added to a molecule to break it apart into two molecules this reaction is called hydrolysis. The term ‘lysis‘ means to break apart, and the term ‘hydro‘ refers to water. Thus, the term hydrolysis means to break apart with water. The reverse of that reaction involves the removal of water from two molecules to join them together into a larger molecule. Since the two molecules are losing water, they are being dehydrated. Thus, the formation of molecules through the removal of water is known as dehydration synthesis. Since water is also a by-product of these reactions, they are also commonly referred to as condensation reactions. As we have seen in Chapter 6, the formation of the major classes of macromolecules in the body (proteins, carbohydrates, lipids, and nucleic acids) are formed through dehydration synthesis where water is removed from the molecules (Figure 7.x). During normal digestion of our food molecules, the major macromolecules are broken down into their building blocks through the process of hydrolysis.

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Figure 7.7 Hydrolysis and Dehydration Synthesis. The reactions of hydrolysis mediate the breakdown of larger polymers into their monomeric building blocks by the addition of water to the molecules. The reverse of the reaction is dehydration synthesis, where water is removed from the monomer building blocks to create the larger polymer structure.

As you learned in Chapter 6, the major macromolecules are built by putting together repeating monomer subunits through the process of dehydration synthesis. Interestingly, the organic functional units used in the dehydration synthesis processes for each of the major types of macromolecules have similarities with one another. Thus, it is useful to look at the reactions together (Figure 7.8)

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Figure 7.8 Dehydration Synthesis Reactions Involved in Macromolecule Formation. The major organic reactions required for the biosynthesis of lipids, nucleic acids (DNA/RNA), proteins, and carbohydrates are shown. Note that in all of the reactions, there is a functional group that contains two electron withdrawing groups (the carboxylic acid, phosphoric acid and the hemiacetal each have two oxygen atoms attached to a central carbon or phosphorus atom). This forms a reactive partially positive center atom (carbon in the case of the carboxylic acid and hemiacetal, or phosphorus in the case of the phosphoric acid) that can be attacked by the electronegative oxygen or nitrogen from an alcohol or amine functional group.

The formation of esters and the related compounds, amides, phosphoesters, and acetals are formed by dehydration synthesis, involving the loss of water. The reaction mechanisms for each of these reactions is very similar. Let’s take a look at the formation of the ester linkage as an example (Figure 7.9).

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Figure 7.9 Reaction Mechanism of Ester Formation. (1) This reaction mechanism is set up by the nature of carboxylic acid functional group. The presence of the carbonyl oxygen and the alcohol functional groups create an electron withdrawing situation, where the electronegative oxygen atoms pull the electrons away from the central carbon atom. This creates a very polar situation, where the central carbon has a strong partial positive character. (2) The strong partial positve character of the central carbon atom of the carboxylic acid attracts one of the lone pair electron groups from the alcohol functional group, shown in red. This enables a new covalent bond to form between the alcohol functional group and the carboxylic acid functional group. This creates an intermediate that has five bonds attached to the central carbon and three bonds attached to the oxygen atom of the incoming alcohol. (3) The intermediate with five bonds to the central carbon is unstable and occupychristmas.orgldn’t normally form, however the presence of the carbonyl oxygen makes the reaction more favorable. It will be able to temporarily absorb the extra electron potential around the central carbon atom, due to its electronegative character and the double bond will temporarily shift up onto the central oxygen forming a lone pair intermediate. (4) The extra lone pair on the carbonyl oxygen shifts back down to reform the double bond with the central carbon. (5) This causes the shared electron pair between the central carbon atom and the original alcohol functional group to shift over to the alcohol, breaking the covalent bond. (6) The extra lone pair of electrons on the free alcohol group take the proton from the new incoming alcohol group forming a molecule of water and the final ester structure.

All of the dehydration synthesis reactions shown for the major macromolecules have a similar reaction mechanism to that shown for the ester bond formation. Notice that the reverse of the reactions show mediate the hydrolysis of the bond linkage by the addition of the water molecule across the bond. This restores the original functional groups, a carboxylic acid and an alcohol in the case of the ester.

Oxidation-Reduction Reactions

An oxidation-reduction (redox) reaction is a type of chemical reaction that involves a transfer of electrons between two atoms or compounds. The substance that loses the electrons is said to be oxidized, while the substance that gains the electrons is said to be reduced. Redox reactions always have to occur together. If one molecule is oxidized, then another molecule has to be reduced (ie. electrons don’t appear out of thin air to be added to a compound, they always have to come from somewhere!).

The change in electron composition can be evaluated in the change of the oxidation state (or number) of an atom. Therefore, an oxidation-reduction reaction is any chemical reaction in which the oxidation state (number) of a molecule, atom, or ion changes by gaining or losing an electron. We will learn how to evaluate the oxidation state of a molecule within this section. Overall, redox reactions are common and vital to some of the basic functions of life, including photosynthesis, respiration, combustion, and corrosion or rusting.

As shown in Figure 7.10, an easy mnemonic for helping you remember which member gains electrons and which member loses electrons is ‘LEO the lion says GER’, where LEO stands for Lose Electrons = Oxidized and GER stands for Gain Electrons = Reduced.

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Figure 7.10. The Rules of Oxidation and Reduction.

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The mnemonic LEO the lion says GER is a helpful way to remember the major concepts of Oxidation-Reduction reactions, noting that when a molecule Loses Elections it is Oxidized (LEO), and when a molecule Gains Electrons it is Reduced (GER).