Mod+8+Reading+Guide

The main idea of Module 8 and Chapter 20 was on the functions and properties of different enzymes and how they are affected by other substances in the body and in the cells.

__**20.1: Enzymes**__ Summary: **Enzymes** are biological catalysts for almost all the chemical reactions that take place in the body. A catalyst increases the rate of a chemical reaction by lowering the activation energy for the reaction (causing less energy to be needed before the reaction can take place). **Enzymes are named** with the suffixes -ase or -in in a way that describes the reactions that they catalyze. Oxidases catalyze oxidation reactions, for example.

Struggling Topic 1: Where does the IUPAC draw the line at official names? Is the IUPAC method for naming proteins the one that simply lists all of the amino acids with their proper suffixes? Is there a method for naming all of these, but because these names are so long we probably use common names much more frequently?

Struggling Topic 2: My students struggle with the idea of whether or not enzymes are __required__ for chemical reactions to take place. I know that the enzyme is not required for the reaction to take place, but I also know that the reactions would be too inefficient without an enzyme as a catalyst. Is there a good example we can use for this? How long would it take our body to digest food without enzymes? Would it be so long that we'd starve to death before we got the energy?

__**20.2 Enzyme Action (quiz questions on this one)**__ Summary: **Substrates** are groups of relatively small reacting molecules that are held in place by the unique 3D shape of the enzyme. An enzyme's **active site** is the region of the enzyme where the substrate can bind to the side chains of the enzyme to catalyze the reaction. For example, an enzyme that catalyzes a synthesis reaction would have an active site that causes the reactants to bind to the enzyme in just the right way so that the reactants are facing each other in the correct orientation. This allows the reaction to proceed more quickly (lowering the activation energy). An **enzyme-substrate (ES) complex** is a combination of enzyme and substrate when the substrate is binded with the enzyme in the proper orientation. This allows a chemical reaction to proceed with less activation energy than is needed without the ES complex. The actions of many enzymes can be described with the **lock-and-key model** that describes the enzyme's active site as rigid and unchanging so that only the proper substrate could bind to it and have a reaction. Other enzymes are better described with the **induced-fit model** that describes an enzyme's active site that interacts with the substrate to make a close fit that provides the proper orientation for the reaction.

Struggling Topic 1: What causes some enzymes to be more flexible such as the enzymes described by the induced-fit model while some are rigid such as those that are described by the lock-and-key model? Is the difference something in the structure of the enzymes?

Struggling Topic 2: Do some enzymes have more than one active site? I remember Mod 7's lab describing hemoglobin and the way it binds to and transports 4 oxygen molecules. Does this mean that hemoglobin is a protein with four active sites?

__**20.3 Factors Affecting Enzyme Activity**__ Summary: An enzyme's **activity** describes how quickly an enzyme catalyzes the reaction converting the substrate into product. The **optimum temperature** is the temperature when enzymes are most active because the particles move quickly so that they can collide with the enzyme's active site most efficiently, but the temperature is not so high as to denature the protein (37 degrees C or typical body temperature). The **optimum pH** for an enzyme is the pH where enzymes are active because the 3D structure of the enzyme maintains the active site where the reaction occurs. At pH levels that are not optimum, the enzyme's activity is diminished because the enzyme changes shape and the active site is disrupted. The concentrations of enzyme and substrate also affect the reaction rate. As the substrate concentration remains constant, increasing the enzyme concentration directly increases the reaction rate. As the enzyme concentration remains constant, increasing the substrate concentration increases the reaction rate to a maximum level of activity - when all the enzymes' active sites are occupied and used as quickly as they can be.

Struggling Topic 1: Does the body usually produce more enzymes to avoid the "ceiling" that is reached when the maximum activity level is limited by the amount of available enzymes in a given reaction? Or is the body okay with functioning at this "ceiling" of maximum activity level given a certain number of available enzymes in a given reaction?

Struggling Topic 2: Does the optimum temperature of enzymes explain why our body temperature is maintained at 37 degrees? How does this work in cold blooded animals? Do they have enzymes with a broader range of optimum temperatures, or do their enzymes only function when the organism is the proper temperature?

__**20.4 Enzyme Inhibition**__ Summary: **Inhibitors** are molecules that cause enzymes to lose their catalytic activity. Some are **irreversible** and cause the enzyme to lose catalytic activity permanently, but many are **reversible** and can be reused when the inhibitor dissociates from the enzyme. A **competitive inhibitor** has a structure that is similar to the substrate so it can bond to the enzyme just like the substrate. As long as the inhibitor occupies the active site, the enzyme cannot function as a catalyst. In this case, if the substrate concentration is increased enough, the inhibitor will eventually dissociate away from the active site, and the substrate will be able to bind with the active site again. A **noncompetitive inhibitor** has a structure that is different from the substrate, and it binds with the enzyme in a way that causes the enzyme to change shape. This causes inhibition because the enzyme's change in shape keeps any substrate from fitting with the distorted shape. Increasing the concentration of substrates will not decrease the inhibition of a noncompetitive inhibitor, but decreasing the concentration of the noncompetitive inhibitor will decrease the inhibition. Most irreversible inhibitors are toxic substances that destroy enzymes such as insecticide, nerve gas, and **antibiotics**. Antibiotics are irreversible inhibitors used to inhibit bacterial growth.

Struggling Topic 1: My life science students struggle to understand whether antibiotics kill bacteria or simply inhibit bacterial growth. I suppose the correct answer is between these two because the antibiotic does keep the bacteria from building cell walls and kills bacteria, but some bacteria is able to resist because of some adaptations. Is this correct? It would be helpful to my students to hear both sides of this in slightly more detail.

Struggling Topic 2: I would assume that the body produces far more reversible inhibitors than irreversible inhibitors because the body usually seems to reuse materials when it can. Is this a fair assumption or generalization?

__**20.5 Control of Enzyme Activity**__ Summary: **Zymogens** or **proenzymes** are produced as an inactive form of an enzyme and stored until needed. When they are needed, they are activated by a reaction that removes a peptide section from the zymogen. This allows enzymes to be produced in one place of the body for use elsewhere such as digestive enzymes that are produced in the pancreas. **Allosteric enzymes** are enzymes that can bind a regulator molecule in addition to the substrate and are the first enzyme in a sequence of reactions leading to an end product. This **regulator molecule** changes the shape of the enzyme's active site to either speed up or slow down the reaction that the enzyme catalyzes. A **positive regulator** speeds up a reaction by changing the shape of the protein to help the substrate bind more easily, and a **negative regulator** prevents the proper binding of the substrate and slows down the rate of catalysis by making it harder for the substrate to bind properly. **Feedback control** is a system where the end product of an enzyme acts as a negative regulator to slow and stop the reaction when sufficient product has been synthesized. For the reaction to continue, the product would need to dissociate elsewhere in the cell.

Struggling Topic 1: A negative regulator is different from an inhibitor, right? The way it was worded in the book made it sound like a "negative regulator prevented the proper binding of the substrate," but I think this means slows down the proper binding of the substrate. In the context I can't tell whether the reaction continues when a negative regulator is being used or not. It might be that the reaction may continue for enzymes that do not have a negative regulator attached to them, or it might be that the reaction continues more slowly than it did even for enzymes with a negative regulator attached to them.

Struggling Topic 2: Are feedback control systems common in our cells? It would seem like this would be the "standard operating procedure" for specialized enzymes that catalyze reactions for specific tasks. It doesn't seem like the enzyme would want to continuously catalyze a reaction unless it was sure the product was being used or needed.

__**20.6 Enzyme Cofactors and Vitamins**__ Summary: **Simple enzymes** are enzymes that need only proteins in their functional forms. Many enzymes need small molecules or metal ions called **cofactors** to catalyze reactions properly. A **coenzyme** is a small organic molecule that acts as a cofactor. **Vitamins** are organic molecules that are essential for normal health and growth but are not synthesized by the body. Vitamins are **water-soluble vitamins** when they have polar groups such as --OH or --COOH, and they are **fat-soluble vitamins** when they are nonpolar compounds. Water soluble vitamins are not stored in the body and are easily eliminated by the urine. Fat soluble vitamins are stored in the body. This means that water soluble vitamins must be in the daily diet, and fat soluble vitamins can be toxic if there is too much stored. Some common water-soluble vitamins include thiamin, riboflavin, niacin, pantothenic acid, pyridoxine, cobalamin, ascorbic acid, biotin, and folic acid. Some common fat-soluble vitamins include vitamins A, D, E, and K.

Struggling Topic 1: How quickly are water-soluble vitamins eliminated from the body? How many days of water-soluble deficiency are needed for a significant health change? Is this one of the major concerns of dieting and nutrition?

Struggling Topic 2: If fat soluble vitamins are stored in the body and can be harmful in large quantities, how are these removed from the body? From what I read it would seem like these aren't removed from the body, but that would cause a certain toxicity level to be reached eventually. Is there a bodily process for breaking down these vitamins when they are approaching a dangerous concentration?

Critique A. specifics about how clearly the author communicated individual topics ->20.1- Great example in the enzyme chart for classification on p. 712. It is easy for me to understand concepts like this when the author puts as much information as she can in one place at a time (like a table/chart/graph/or other image)

B. specifics about the amount of content and whether it was sufficient to help learn the material (did you need more examples?) ->20.2 - the example of an ES complex using sucrose and the enzyme that breaks sucrose into two parts did a good job of showing how an ES complex works and how the enzyme is then reusable after the reaction has been completed. -> 20.5 - I needed more examples to show the difference between a negative regulator and an inhibitor. These sounded too similar. It sounded like both bind to the enzyme and prevent the active site from working as it normally would.

C. why did the author place this chapter where she did in the overall text? not later or earlier, transitions with previous chapter, with subsequent chapter(s), did this chapter seem out of place?