Spontaneous Changes/Thermodynamics

We have seen that metabolic reactions involve changes in energy: anabolism requires energy while catabolism releases energy. Different types of reactions follow predictable patterns and can be grouped using this definition. Yet, considering if a reaction occurs needs more information. As you read this next section look for details about the amount of energy needed to activate a reaction. You will use this information later in this Activity.

We know from experience that paper can burn in a combustion reaction that releases large amounts of energy. Only two reactants are needed for this reaction: paper and oxygen.  Yet, we constantly keep paper exposed to the oxygen in air. The reactants are there but combustion does not happen spontaneously. In order to get the reaction to start, an energy source, like a flame, is needed.

On the other hand, the classic elementary school volcano demo involves a double displacement reaction.

Scientists who study energy changes have noticed that, in general, catabolism is a spontaneous process. Disorder is more natural than large, organized structures. The paper is more organized on a molecular level than the ashes it makes when burned. Likewise, the volcano demo creates a disorganized chemical mess. 

As we know, the paper will burn if it gets hot enough, like with the help of a flame. The thermal energy added is sufficient to start the combustion reaction. The energy released from this catabolic reaction is enough to keep the paper burning until the paper is  used up. In the volcano demo, the room temperature is sufficient to both start and continue the double displacement reaction until the reactants are used up.  The difference in spontaneity, therefore, is the amount of energy needed to activate the first molecules to react. 

In cells, most biochemical reactions are not spontaneous. In other words, even if the two reacting molecules are present in the same location in the cell, they won’t react without being activated. If the reaction requires energy we describe it as an endergonic (definition: Endergonic reactions require energy to occur, whereas endothermic reactions require specifically heat to occur.) reaction. It is the opposite of exergonic (definition:Exergonic reactions release energy as they occur, whereas exothermic reactions release specifically heat as they occur.)reactions. Let's connect some of the biochemical reactions we learned about in the previous Activity to energy change.

As you learned in the first Unit, enzymes are a special group of proteins. They help to speed up biochemical reactions. Specifically, they help make non-spontaneous processes become spontaneous by reducing the amount of energy needed to activate the first molecules to react. For example, in cellular respiration, glucose can combine with oxygen to release large amounts of energy.

Three-Dimensional Shapes

In the last unit we saw that the shape of a protein is important for its function. This is especially true for enzymes. Let’s explore this further to see how small differences in shape or how reactants interact with an enzyme affect the enzyme’s function.

For this activity you’ll need a $5 bill (or other denomination) or a similarly sized rectangular piece of paper. You’ll also need two paper clips. The following video tells you how to set up the reaction. For the purpose of this investigation, the folded up money represents an enzyme and the paperclips are the reactants. 

The structure of an enzyme is important for its function. This video summarizes some of these details. 

We will explore more of these details in this Activity.

Enzyme Structures

The biochemists that study enzymes use the term substrate (definition:a reactant used by an enzyme or other protein in a biochemical process.)instead of reactant in  biochemical reactions. This may seem like a strange distinction, but it helps biochemists describe biochemical reactions differently from how chemists describe chemical reactions. We will use the term substrate here for this reason.

All enzymes are composed of a specialized region called the active site. (definition: a region in an enzyme that performs a biochemical reaction.) The active site is where the biochemical reaction occurs. It’s formed by the tertiary or quaternary structure of the enzyme. Click on the image below to explore the shape of the enzyme pepsin and see its active site.

The shape of the active site is important to how it functions. Also, interestingly, the shape of the active site changes before, during and after a biochemical reaction. We describe these changes as the induced fit of an active site with its substrate. Watch this video to see how the shape of the active site changes. 

It’s important to note that enzymes do not get used up in a reaction. After the products are made, the enzyme is ready to react again with new substrate. Check your understanding with the interactive below. Drag each word as it appears on the left and drop it in the box at its proper location. Click the submit button to check your answers.

U2A2Quiz

Long Description

The shape of the active site makes enzymes very specific. In fact, most enzymes only react with one substrate molecule for this reason. This specificity helps enzymes to be used by cells for a specific function. You can explore how the subunits of the enzyme ATP synthase work together to change the shape of the active site below in this animation from St. Olaf College. 

ATPSynthase

Long Description

Rates of Enzyme Activity

In the previous video we could see that the rate of an enzyme reacting generally increases with a factor like temperature. This should make sense because this pattern is true for many other physical and chemical changes. Increased thermal energy means that the molecules involved in the change come together and collide more often and with more energy.

In addition to changes in temperature, protein structure is sensitive to changes in pH. Notice that for most species only a narrow pH range is suitable for life.

Remember that some amino acids have hydrophilic R-groups. They are able to interact with each other and water molecules to make strong intermolecular forces of attraction. They are also able to interact with acids and bases in the surroundings.

Let’s explore the effect of temperature changes on the shape of proteins, including enzymes.

Let’s take a closer look at how intermolecular forces of attraction can change because of changes in temperature or pH. The animation will autorun so you do not need to click on the Continue buttons when they appear (Source: Association of the British Pharmaceutical Industry).

 

In order to protect the shape of proteins and enzymes, organisms have evolved adaptations to prevent denaturation. Cells contain a lot of water. Water can absorb large amounts of energy before increasing its temperature, so cells use water to absorb heat instead of their proteins.  We will explore other temperature control adaptations later in the course.

Changes to pH are regulated with buffers. (definition:a chemical that prevents changes in pH.) Buffers have a unique property in that they can act like an acid or a base. For this reason we describe buffers as amphoteric. (definition:a molecule with both acidic and basic functional groups in the same molecule.) A reaction we haven’t looked closely at yet, neutralization, (definition:a reaction between an acid (low pH) and a base (high pH) producing a more neutral product.) involves an acid combining with a base. The products usually have a pH close to neutral, pH 7. Buffers can therefore combine with either an acid or a base to prevent changes pH. To see this in action explore the following animation adapted from Durham County Community College.

BufferingSolutions

Long Description

Enzymes Involved in Diseases

Enzymes are essential to the proper running of our body’s physiological processes. If something goes wrong with one of these enzymes this often leads to a disease. One of the reasons Biologists study enzymes is to learn more about diseases caused by enzyme malfunctions. As more is understood about how enzymes work, including details about their active sites, Biologists hope to be able to find treatments for patients with these diseases.

Targeted Control of Enzymes

Denaturation is one way to turn off enzyme activity. For example, in the digestive system, different organs have different pH values. The mouth is around pH 7, the stomach pH 2, and the small intestines around pH 8. Enzymes in each organ function best at the pH of the organ. As food moves through the digestive system, enzymes can move as well. Salivary amylase, for example, can move into the stomach where it becomes inactive because the highly acidic environment denatures it. New saliva is made to replace the lost enzymes.

From an energy perspective, however, this method of inactivating enzymes is not very efficient: energy and resources are used to make new enzymes. A more targeted control of enzymes involves activating (definition:a method of turning on a biochemical process.) or inhibiting (definition:a method of turning off a biochemical process.) the enzyme without destroying it.

There are many different methods of activating or inhibiting an enzyme. Each of them describe an elegant way in which nature makes subtle changes to the molecule. Since we will be looking closely at specific enzymes in the course, let's examine just a few methods of inhibition and activation.