Name: factors that shape enzyme function
Uploaded: 2019-01-29T11:04:45.000Z
Duration: 4 min 35 s
Channel: JoVE

K12 Standards

Florida Department of Education

High School

Life Science

SC.912.L.18

SC.912.L.18.4

Enzyme Activity

European explorers had adequate knowledge, skills and equipment, but why didn&#39;t they reach the New World until the end of the 15th century? You&#39;ll be surprised to learn that the answer to this question is related to the small biological molecules called enzymes, that act as catalysts. 

What is a catalyst? It is a substance that enables a reaction to occur faster, using less energy. If you plotted a graph of the energy needed for an uncatalyzed biological reaction, it would look something like this. This height represents the activation energy, which is the minimum amount of energy needed for the reaction to proceed. Enzymes, working as a catalyst, provide an alternate reaction pathway, with a lower activation energy. 

So, how do enzymes actually work? Most enzymes are proteins. The part of their structure which interacts with the molecules they catalyze, is called the active site, which has affinity for only certain substrates and won&#39;t bind with others. When the correct substrates enter the active site, the enzyme changes its shape to attain a higher affinity configuration. This transition state facilitates the reaction and converts the reactants into products. The enzyme, however, has a lower affinity for the products so it releases them and returns to its original shape, ready to repeat the same process. This is an example of a catabolic enzyme because it took a single substrate and broke it to form multiple products. The opposite of this, is the anabolic enzyme, which takes two substrates and joins them together to make a larger product. 

There are numerous other ways that enzymes function. For instance, this enzyme transfigures a single substrate into a new shape. Whereas this one, transfers part of one substrate, onto another. Some enzymes cannot catalyze reactions on their own and require cofactors or coenzymes in order to catalyze their reaction. 

So, you might be wondering, how does all this relate to the 15th century voyages? At that time, sailors didn&#39;t have access to fresh produce containing vitamin C, a coenzyme essential for collagen synthesis. Because of that, the sailors would develop scurvy, a vitamin C deficiency disease, which was often fatal. They solved this problem by pickling vitamin C-rich fruits and vegetables. Pickling reduced the pH of the food, which prevented the activity of microbial enzymes, responsible for rotting them. Therefore, destruction of microbial enzymes and the saving of an essential coenzyme, played a major role in the success of long expeditions. 

In this lab, you can quantify how different conditions affect enzyme function, by assessing the reaction rate, the amount of product made, per unit time. You&#39;ll first measure the baseline reaction rate at a standard room temperature and neutral pH. The rate will increase at the beginning until all of the enzyme molecules are completely saturated with the substrate. And then, the catalysis will reach a steady level as the enzymes are busy continuing the cycle of binding substrate, catalysis and release. Once the baseline reaction rate has been established, it can be used as reference point for other conditions. The enzyme that you&#39;ll work with in this lab is turnip peroxidase. You&#39;ll evaluate its activity under varying values of temperature and pH.

enzyme activity

<h4>Biological Catalysts</h4>

All living organisms continuously perform numerous biochemical reactions to sustain their presence. Most of these reactions require an input of energy to start, which is called the activation energy. Catalysts are chemicals that lower the activation energy. Even though catalysts facilitate a chemical reaction, they are not consumed by it. This means a catalyst can facilitate a specific chemical reaction over and over in succession, increasing the rate of that reaction.

Enzymes are biological catalysts that increase the speed and efficiency of biochemical reactions. Most enzymes are proteins but certain ribonucleic acid molecules also have catalytic properties. Each type of enzyme can only bind to one or a few specific substrates, therefore, there is a vast diversity of enzymes, all with distinct functions. The specific reaction of an enzyme depends on its active sites, which has shapes that closely matches the shape of its substrates. Upon substrate binding, the enzyme changes shape slightly in a way that allows the chemical reaction to happen more readily, thus reducing the activation energy of the reaction. Once the reaction takes place, the enzyme releases the products and returns to its original shape, which allows it to repeat the process again.

<h4>Catabolytic versus Anabolic Enzymes</h4>

Most enzymatic reactions can be categorized as either catabolic and anabolic, which have opposite functions. Enzymes that mediate catabolic reactions break down larger substances into multiple products. A well-known catabolic enzyme is lactase, which splits the disaccharide lactose in dairy products into monosaccharides galactose and glucose. Humans have large amounts of lactase in their small intestine after birth, however many individuals lose more than 90% of their lactase by early childhood1. This reduction diminishes the ability to digest lactose in an age-dependent manner, which is known as lactose intolerance2.

Anabolic enzymes combine multiple substances into a single product. For example, the enzyme DNA polymerase synthesizes DNA molecules by joining nucleotides together. Similarly, the enzyme glycogen synthase connects glucose molecules to generate glycogen. Insulin regulates the activity of glycogen synthase, therefore diabetic patients with low to no insulin levels cannot synthesize glycogen without insulin treatment3.

<h4>Environmental Factors</h4>

The shape and charge of the active site of an enzyme is tailored to the specific chemical reaction it catalyzes, therefore the enzyme activity is influenced by factors that affect its active site. Hence, enzymes require specific conditions to work at optimal levels and depending on their function and location, these conditions can vary greatly. These factors include pH and temperature. For example, active sites of enzymes often contain acidic or basic amino acids. Deviations from the optimum pH alter the charges in the active site, making it difficult for the substrates to interact with the enzyme. This property has been used for centuries to preserve food by pickling, which reduces the pH of the pickled food item to a level that effectively inhibits microbial enzymatic activity. Similarly, each enzyme works at an optimal temperature range. If the temperature shifts below or above this range, it alters the shape of the active site, preventing it from effectively interacting with its substrates. In most cases, returning to the optimal temperature restores the enzyme&#8217;s original shape and function, however, temperatures that are too high can denature or irreversibly damage the enzyme structure. Again, these properties are useful for food safety; we cook meat thoroughly to kill harmful bacteria by denaturing their enzymes and refrigerate most food items to slow down enzymatic activity of microorganisms.

Extremophiles, or organisms found in extreme conditions that are lethal to most forms of life, have enzymes capable of functioning at those extremes. For instance, Thermus aquaticus is a bacterium found in hot springs and hydrothermal vents reaching temperatures at which most proteins would denature. Taq polymerase is a thermostable DNA polymerase found in T. aquaticus, which has allowed the development of polymerase chain reaction (PCR), a widely-used laboratory method for rapid DNA replication. PCR requires high temperatures to separate the strands of the DNA double helix to be replicated. Taq polymerase remains stable at these high temperatures while most enzymes would be degraded. PCR cycles between high temperatures that break the DNA into single strands and lower temperatures that allow the polymerase to build new double stranded DNA.

<h4>Molecular Factors that Influence Enzyme Activity</h4>

In addition to specific pH and temperature ranges, some enzymes function better in the presence of other molecules or ions. Coenzymes are biomolecules that bind to the active site of the enzyme and participate in catalysis without getting consumed by the reaction. Coenzymes often transport electrons, specific atoms and functional groups, and thus act as intermediary carriers. B vitamins act as coenzymes for numerous biochemical reactions. For instance, coenzyme A (coA), which is the active form of pantothenic acid, is required by 4% of all mammalian enzymes4. Cofactors are often classified as inorganic substances, such as ions, that are required for the enzymatic function. For example, all DNA polymerase enzymes require Mg2+ or Mn2+ for DNA replication as well as excision of incorrectly incorporated nucleotides5.

There are also other molecules that are not necessary for an enzyme to function but are capable of altering the enzymatic activity. Substances that increase the enzyme activity are called activators, whereas others that decrease the enzyme activity are called inhibitors. These molecules bind to enzymes either at the active site or other locations on the enzyme known as allosteric sites. Sometimes these molecules can bind to the exact location in the active site as the substrate, and thus compete with the substrate for the enzyme binding. Others, especially the substances that bind to allosteric sites, can alter enzyme function without blocking the substrate binding to the active site, and are thus non-competitive. Moreover, binding of inhibitors can be reversible or irreversible. When the interaction is reversable, the enzyme can resume its function once the inhibitor detaches. However, when the binding is irreversible, the inhibitor never detaches from the enzyme and the enzyme becomes irreparably damaged and needs to be replaced. Nevertheless, enzyme inhibitors are useful as well. For instance, inhibitors have been utilized as antibiotics to inhibit bacterial growth, and as chemotherapeutics to inhibit the uncontrolled division of cancer cells6.

<h4>Measuring Enzyme Function</h4>

One method used by scientists to study the effects of different conditions on enzyme function is to quantify the reaction rate, which is how fast the enzyme is catalyzing the reaction. Therefore, a higher reaction rate indicates that the enzyme is catalyzing reactions more efficiently, whereas a lower rate means that it is working less efficiently. To determine the reaction rate, the reaction velocity is calculated by measuring the amount of product made per unit time. This is done by measuring the product concentration starting right at the beginning of the reaction when the product concentration is increasing linearly, until the enzyme is completely saturated with the substrate and the catalysis reaches a steady level. Once the baseline reaction rate is determined, it can be used as a reference point, or control, when comparing between a variety of treatments. We can assess reaction rates as relative or absolute measures. A relative reaction rate is a comparative measure that shows differences between two or more conditions, such as treatments in a single experiment, but does not give a value for what is being measured. An absolute reaction rate relies on a quantitative measure of the progress of the reaction. An easy way to understand the difference between relative and absolute reaction rates is to consider measuring the speed of a car in a race. A relative method would compare by assessing the ranking of cars at the finish line, whereas the absolute rate would assess and compare the speed of individual cars in miles per hour.

Since enzymes are so widely used, researchers have begun looking for ways to create and modify enzymes to suit specific needs, known as protein engineering. Recombinant DNA technology allows amino acid sequences to be changed in order to alter an enzyme&#8217;s shape or active site affinity. This has been used to create highly sensitive diagnostic tests for various conditions, as well as for bioremediation efforts and waste management tools7.

<h4>References</h4>

<ol class="references">
	<li>Swagerty DL Jr, Walling AD, Klein RM. Lactose intolerance. Am Fam Physician. 2002, Vol. 65, 9: 1845-50.</li>
	<li>Lomer MC, Parkes GC, Sanderson JD. Review article: lactose intolerance in clinical practice--myths and realities. Aliment Pharmacol Ther. 2008, Vol. 27, 2: 93-103.</li>
	<li>AR, Saltiel. New perspectives into the molecular pathogenesis and treatment of type 2 diabetes. Cell. 2001, Vol. 104, 4: 517-29.</li>
	<li>DO, Kennedy. B Vitamins and the Brain: Mechanisms, Dose and Efficacy--A Review. Nutrients. 2016, Vol. 8, 2: 68 doi:10.3390/nu8020068.</li>
	<li>Vashishtha AK, Wang J, Konigsberg WH. Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases. J Biol Chem. 2016, Vol. 291, 40: 20869-20875.</li>
	<li>Watson ID, Stewart MJ, Platt DJ. Clinical pharmacokinetics of enzyme inhibitors in antimicrobial chemotherapy. Clin Pharmacokinet. 1988, Vol. 15, 3: 133-64.</li>
	<li>Ahuja SK, Ferreira, GM, Moreira AR. Utilization of Enzymes for Environmental Applications. Crit Rev Biotech. 2004, Vols. 2-3, 125-54.</li>
</ol>

Biological Catalysts

All living organisms continuously perform numerous biochemical reactions to sustain their presence. Most of these reactions require ...

Education

JoVE Lab Manual

Biology

Cellular Processes

factors that shape enzyme function

Enzymes are biological catalysts that help living things run biochemical reactions faster. They lower activation energy, which is the energy needed to start a reaction. Enzymes are not used up in the process, so they can keep working again and again. Most enzymes are proteins, although some ribonucleic acid molecules also have catalytic activity.

Each enzyme usually binds only one or a few specific substrates. This selectivity depends on the enzyme’s active site, which fits its substrate like a matching shape. When the substrate binds, the enzyme changes shape slightly and makes the reaction easier. After the products form, the enzyme releases them and returns to its original shape.

Enzyme reactions are often grouped as catabolic or anabolic. Catabolic enzymes break larger molecules into smaller products. Lactase is a catabolic enzyme that splits lactose in dairy products into galactose and glucose. Many people lose most of their lactase by early childhood, which can lead to lactose intolerance. Anabolic enzymes build larger molecules from smaller parts. DNA polymerase joins nucleotides to make DNA, and glycogen synthase links glucose molecules to form glycogen. Insulin helps regulate glycogen synthase, so people with little or no insulin may need treatment to make glycogen normally.

Enzyme activity depends on conditions such as pH and temperature. Many active sites contain acidic or basic amino acids, so changes in pH can alter charge and make substrate binding harder. Pickling uses this idea by lowering pH and slowing microbial enzyme activity. Temperature also matters because each enzyme has an optimal range. Low or moderate shifts may slow the enzyme, but high temperatures can denature it and cause lasting damage. Cooking meat and refrigerating food both reduce harmful microbial activity in this way. Extremophiles live in harsh environments and have enzymes that still work there. Thermus aquaticus is one example, and its Taq polymerase stays stable in the high heat used for PCR, a method that copies DNA by cycling between hot and cooler temperatures.

Some enzymes also need coenzymes or cofactors. Coenzymes are biomolecules that help the reaction and are not consumed. They often carry electrons, atoms, or functional groups, and many B vitamins serve this role. Coenzyme A, the active form of pantothenic acid, is needed by many mammalian enzymes. Cofactors are usually inorganic substances, such as ions. DNA polymerase, for example, requires Mg2+ or Mn2+ for DNA replication and for correcting some mistakes.

Other molecules can change enzyme activity without being required for the reaction. Activators increase activity, while inhibitors decrease it. These molecules may bind at the active site or at allosteric sites, which are different locations on the enzyme. Some inhibitors compete with the substrate for the active site, while others act in a non-competitive way by binding elsewhere. Inhibitor binding can also be reversible or irreversible. Reversible inhibitors can detach and let the enzyme work again, but irreversible inhibitors permanently damage the enzyme. Scientists use enzyme inhibitors as antibiotics and as chemotherapeutic agents to limit cancer cell division.

Scientists measure enzyme function by looking at reaction rate, or how fast product is made. A faster rate means the enzyme is working more efficiently. Reaction velocity is measured by tracking product concentration over time, usually from the start of the reaction until the enzyme becomes saturated with substrate and the rate levels off. Researchers use that baseline as a control when comparing different treatments. Reaction rates can be reported as relative or absolute values. Relative rates compare conditions, while absolute rates give a direct quantitative measure, much like comparing race rankings versus miles per hour.

Because enzymes are so useful, researchers also engineer them for special tasks. Protein engineering uses recombinant DNA technology to change amino acid sequences and adjust enzyme shape or active site binding. This approach has helped create sensitive diagnostic tests, as well as tools for bioremediation and waste management.

Factors That Shape Enzyme Function

photosynthesis

Photosynthesis: Light, Sugars, and Carbon

Photosynthesis turns sunlight into chemical energy in the form of glucose. This process powers most life on Earth by helping autotrophs, or primary producers, make food. The glucose they make can provide quick energy or be stored as starch for later use. Consumers depend on these producers for energy. Photosynthesis happens in many kinds of organisms. Cyanobacteria, some protists such as algae, and plants can all carry out this process. In eukaryotic cells, it takes place in the chloroplast.

cellular respiration

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Enzymes are biological catalysts that help living things run biochemical reactions faster. They lower activation energy, which is the energy needed to start a reaction. Enzymes are not used up in the process, so they can keep working again and again. Most enzymes are proteins, although some ribonucleic acid molecules also have catalytic activity. Each enzyme usually binds only one or a few specific substrates. This selectivity depends on the enzyme’s active site, which fits its substrate like...

cellular processes

Explore how pH, temperature, inhibitors, cofactors, and substrates affect enzyme function, plus examples like lactase, Taq polymerase, and PCR.

Factors That Shape Enzyme Function | JoVE K12

SC.912.L.18.11

Prepare turnip peroxidase and test how pH and temperature affect enzyme activity using buffer solutions, hydrogen peroxide, and guaiacol in this high school lab.

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Measure turnip peroxidase activity using guaiacol, then compare reaction rates across pH 3-8 and temperatures from ice bath to 60 °C.

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SC.912.L.18.9

A. All living things are composed of four basic categories of macromolecules and share the same basic needs for life.

B. Living organisms acquire the energy they need for life processes through various metabolic pathways (primarily photosynthesis and cellular respiration).

C. Chemical reactions in living things follow basic rules of chemistry and are usually regulated by enzymes.

D. The unique chemical properties of carbon and water make life on Earth possible.

Factors That Shape Enzyme Function

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