Unit 2 test scheduled for 5 October.
You have already learned that most chemical reactions that occur in cells (metabolism) require the assistance of enzymes. These catalysts facilitate the chemical reaction by lowering the activation energy needed to bring the reactants together. Most enzymes in our cells are proteins. However, recent research has demonstrated that some RNA molecules also function as enzymes. In this unit you will learn how protein enzymes carry out their catalytic functions and the factors that influence their activity. To do that you will first need to review and expand your understanding of some basic principles of energy and thermodynamics.
Learning Objectives: The successful student will be able to ...
- explain the difference between potential and kinetic energy and describe biologically relevant examples.
- list and describe different forms of energy (chemical, light, mechanical, etc.) in biological systems.
- state the Law of Conservation of Energy and the Law of Kinetic Energy of Matter.
- state the first and second Laws of Thermodynamics and apply these concepts to biological systems.
- explain the concept of entropy in relation to energy transfer in chemical reactions and the laws of thermodynamics.
- describe the difference between an endergonic and exergonic reaction and describe the changes in free energy and entropy during these reactions.
- explain how the 3D shape of enzymes is an important factor in the function of these catalysts.
- describe, using specific examples, the influence of environmental factors on enzyme efficiency including pH, temperature, and substrate concentration.
- construct and use Michaelis-Menton graphs to compare the behavior of different enzymes or enzymes in different environmental conditions.
Lesson One: The basics.
Most of this should be review from previous courses. If not use the links at the end of this lesson to catch up. Recall that energy is defined as the ability to do work. The SI units for energy are joules (J) although in biology kilocalories (kcal) are more commonly used. Be sure that you can describe the difference between stored or potential energy and energy of motion or kinetic energy. Very important for our study of biology is the observation that one form of energy can be converted into another (e.g. potential into kinetic, light into chemical, etc.). As we study this unit and the units on cell respiration and photosynthesis you will see repeated examples of this. You undoubtedly have learned the Laws of Conservation of Mass and Conservation of Energy. Einstein famously showed that mass and energy are interchangeable. In addition, recall the Kinetic Theory of Matter that states that atoms/molecules are in a constant state of motion and the velocity of that motion is related to the energy of the atoms/molecules. These laws and theories become important in our studies of enzymes and biological reactions.
Helpful links.
The Physics Classroom
MSN Encarta-Energy
Chem1 Virtual Textbook
Online Biology Book
Lesson Two: Thermodynamics.
This topic is far too complicated to do anything but scratch the surface of this topic, but there are some important concepts you need to understand. Thermodynamics is the study of how energy behaves, especially when it changes. There are four laws of thermodynamics; one and two are most important for us. Stated in a general non-mathematical form they are:
- In a closed system energy cannot be created or destroyed, but it can be converted from one form into another.
- As energy is converted from one form into another some of the potential energy is lost as heat and the "randomness" (measured as Entropy) of the system increases.
Recognize that the first law is a more formal restatement of the Law of Conservation of Energy. You will see these laws stated in many different ways but they all amount to the same principle. A closed system is one in which there is no net gain or loss of energy to the outside of the system. Presumably the universe is a closed system. Biological systems such as cells, organisms, population, and ecosystems are not.
Go to Essential Biochemistry and work through the first three sections of the thermodynamics review. Be sure that you understand the relationship of the Laws of Thermodynamics to the examples used on these pages and the answers to the review questions.
Homework, due 14 September. Study the photograph of a mushroom growing on a dead tree. In your own words explain how the relationship between the tree and fungus is an example of the Laws of Thermodynamics. In particular, explain what is happening to the entropy of the log and of the mushroom as their relationship progresses and where energy is moving to and from in this situation. Email the answers using your Fontbonne account.
Photo from the blog Everything About Mushrooms.
Lesson Three: Energy considerations in chemical reactions.
In chemistry you learned about endergonic (or endothermic) and exergonic (or exothermic) reactions and the role of energy (e.g. heat) in the formation of the products from the reactants. We will expand on this a bit using the laws of thermodynamics. The molecules of the reactants and products have a certain amount of energy associated with them. Their energy levels are almost never equal (certainly not in biological systems). Recall that energy is released with the products of an exergonic reaction. Use the laws of thermodynamics to consider what this must mean about the amount of energy in the products compared to the initial reactants. Energy is added to the reactants of an endergonic reaction. Again what do the laws of thermodynamics require in terms of the energy associated with the reactants compared to the products? The energy in a molecule available to do work is called Gibbs free energy (G). More important for us, the change in this free energy during a chemical reaction is called ΔG which can be positive or negative.
Go to Kimball's pages and read the section on "Bond Energy" and the decomposition of water into hydrogen and oxygens gasses and the reverse synthesis reaction. Be sure you understand how the laws of thermodynamics are related to the the free energy of reactants vs products in these reactions and to the sign of ΔG. Return to Essential Biochemistry and complete section 4 of the thermodynamics review.
Homework, due 16 September. What are the reactants and the products of photosynthesis. Is this process endergonic or exergonic and what sign would you expect ΔG to have and why? Answer the same question for the process of cell respiration. Email the answers using your Fontbonne account.
Lesson Four: Activation energy and enzyme function.
By now you know that enzymes are cellular catalysts that facilitate the chemical reactions of metabolism. In this and the next lesson we will focus on how enzymes actually function, what environmental factors influence their efficiency and how to quantify their activity. Go to the Online Biology book and read the section on enzymes. You will find a diagram similar to the one below. Recognize this as a exergonic reaction (why is this so?). Notice that although the free energy of the reactants is higher than that of the products, this reaction will not proceed until a small amount of extra energy is added to the reactants. This extra energy is called the "activation energy" or "energy of activation." As you study the diagram and the text determine how the presence of an enzyme affects the magnitude of the activation energy and the change in free energy, ΔG.
Image from Biology, Thomson Learning, Inc.
This reduction in activation energy is vital in biological systems. Think about how you managed to run most of the chemical reactions in your chemistry labs; you added a great deal of heat. Most of the reactions that take place in cells would require the same treatment if it were not for the presence of enzymes. Consider this and the suggestion by scientists that speculate about the initial origin of life on Earth have suggested that enzymes were among the first proteins to evolve; possibly even before the first cells emerged (others have suggested RNA molecules were the first enzymes).
Homework, due 20 September. Email the answers to the following questions using your Fontbonne account.
- In an exergonic reaction, what effect does the presence of an enzyme have on the magnitude of the activation energy? Explain.
- In an exergonic reaction, what effect does the presence of an enzyme have on the change in free energy, ΔG? Explain.
- Consider the graph of a typical endergonic reaction. Do you see the characteristic "hill" representing the activation energy? Explain (hint: think of the entire graph as representing one big activation energy requirement.)
Lesson Five: Reaction sites and environmental factors.
Return to the Online Biology text and read the section on substrates binding sites (also called active sites). Also, view this animation and this animation for a more graphical presentation of this concept. Be sure you appreciate the role the 3D shape of the enzyme plays in the formation and specificity of the active site. Relate this to the secondary and tertiary structure of proteins you studied in the "Macromolecules" unit. You will see one example after another of proteins functioning in cells by this sort of shape change.
In addition to showing a high degree of specificity for their substrates, enzymes also often have very specific environmental requirements; especially temperature, pH, and concentrations. Read more on this in Kimball and in the Online Biology textbook.
Homework, Due 23 September. Go to the tutorial dealing with the enzyme carboxypeptidase and answer the three questions you will find there. You will probably have to go back to some of the information in Unit 1 to review some of the details of amino acid structure. Email the answers using your Fontbonne account.
Lesson Six: Enzyme kinetics.
The study of enzymatic activity under different conditions is called "enzyme kinetics." This field can be highly mathematical as scientists try to develop models to quantify the behavior of enzymes. In this lesson you will study some of the very basic principles of enzyme kinetics and learn how to use this information to compare the activity of enzymes in different experimental situations. Go to the animations from Wellesley College.
View the first two animations, "initial velocity" and "initial velocity 2." Be very sure you understand the basic relationship in these time vs product graphs; the relationship between the initial concentration of the substrate and the slope of the graph (initial velocity) of the enzyme's ability to convert substrate to product (the concentration of enzyme is always held constant).
Now view the "initial velocity 3" animation. Here all the time vs product graphs are distilled into a single substrate concentration vs initial velocity graph. Carefully consider what this graph shows you about the speed at which a given amount of enzyme can convert a substrate into product depending on the concentration of that substrate. This is important! (it should also make common sense).
Now for some math. The Michaelis-Menton animation shows how two values can be determined directly from these graphs. The Vmax value is the velocity value at the point where the curve is leveling off and V1/2 max is simply half that velocity. The most important value now is determined by finding the substrate concentration [S] that corresponds to V1/2 max. This is called the Michaelis-Menton constant, Km. This constant can be used as a single value to compare the efficiency of an enzyme under different conditions or to compare one enzyme to another. Km is calculated from V1/2max rather than Vmax because it is difficult to calculate Vmax directly from the graphs (although with a little more math this is often done; see the last animation if you're interested). For another presentation of this material, see Kimball.
Homework, Due 29 September. Go to Kimball's page on enzyme kinetics. Review if necessary the information on constructing the Michaelis-Menton graphs (substrate concentration vs initial velocity) and the Km constant. Don't worry about the section on calculating Vmax. Read the section on competitive and noncompetitive inhibitors. These are molecules that interfere with enzyme activity either as natural regulators or as metabolic poisons. Michaelis-Menton graphs are often used to quantify the action of these inhibitors.
Kimball outlines three experiments with the enzyme diphenol oxidase, a control, with a competitive inhibitor, and with a noncompetitive inhibitor. Use the substrate concentration [S] and initial velocity, Vi, data to construct three Michaelis-Menton graphs. Estimate Km for each. Write a brief summary describing the effect of the inhibitors on the shape of the graphs and Km.
Helpful (?) websites:
- view the enzyme, diphenol oxidase or catechol oxidase, in the FirstGlance program.
- learn more about this enzyme at Proteopedia.
