Biology (9700) | Mode of action of enzymes

🏹 Chapter 3.1: Mode of Action of Enzymes 🏹

Hello future Biologist!

Enzymes are arguably the most important molecules in your body—they are the tiny, hardworking heroes that make life possible! If your cells didn't have enzymes, chemical reactions would happen so slowly that you would literally freeze (metabolically speaking!).

In this chapter, we are diving into the fascinating details of how these biological catalysts work, focusing on their structure, their incredible specificity, and the two major models used to describe their action.

1. What are Enzymes? (A Quick Review)

Definition and Structure (3.1.1)

Remember from Topic 2 that enzymes are a specific type of protein.

• An enzyme is a biological catalyst: a substance that increases the rate of a chemical reaction without being used up itself.
• Enzymes are globular proteins. This means they are folded into a compact, roughly spherical shape and are generally soluble in water.

Where They Work: Intracellular vs. Extracellular

Enzymes operate in specific locations, which determines their classification:

• Intracellular Enzymes: These work inside the cells.
  Example: Enzymes involved in respiration (like those in the mitochondria) or protein synthesis.
• Extracellular Enzymes: These are secreted and work outside the cells.
  Example: Digestive enzymes like amylase (which breaks down starch) or trypsin (which breaks down protein) found in the gut.

2. The Core Mechanism: Lowering Activation Energy (3.1.2)

The Substrate and the Active Site

The molecules that an enzyme acts upon are called substrates.

The specific region of the enzyme where the substrate binds is called the active site. The active site is a small, specific pocket or groove formed by the folding of the enzyme’s polypeptide chain.

The Key Function: Activation Energy

For any chemical reaction to start, energy is required—this initial energy barrier is called the Activation Energy (\( E_a \)).

Analogy: Think of a reaction as pushing a boulder up a small hill. The Activation Energy is the height of that hill. Once you push it over the top, it rolls down the other side (forming the product) easily.

Enzymes lower this hill. By binding to the substrate, the enzyme provides an alternative reaction pathway that requires much less energy. This allows the reaction to occur quickly at body temperature, where otherwise it would be too slow.

Step-by-Step Enzyme Action

This is the crucial sequence of events you must know:

1. The substrate collides with and binds to the active site of the enzyme.
2. They temporarily form the Enzyme-Substrate Complex (ESC). This is where the magic happens—the substrate is held in the optimal position for the reaction to occur, and its bonds may be stressed or twisted.
3. The reaction proceeds (bonds are broken or new bonds are formed).
4. The substrate is converted into products.
5. The products detach from the active site.
6. The enzyme is now free to bind to another substrate molecule and repeat the process. It remains chemically unchanged.

3. Explaining Specificity: Two Hypotheses (3.1.2)

Enzymes are highly specific—often, one enzyme will only catalyse one particular reaction, or a very small group of similar reactions. This specificity is entirely due to the unique, complementary shape of the active site.

Hypothesis 1: The Lock-and-Key Hypothesis

This model was proposed first (by Emil Fischer in 1894).

• Core Idea: The active site of the enzyme is a rigid structure, perfectly complementary to the substrate, much like a specific key fits a specific lock.
• Specificity: This explains why only one substrate can fit—if the shape doesn't match exactly, the reaction cannot happen.
• Limitation: This model suggests the enzyme is stiff and unchanging, which doesn't fully explain all experimental observations about how enzymes work.

Hypothesis 2: The Induced-Fit Hypothesis (The Modern View)

This model (proposed by Daniel Koshland in 1958) is the currently accepted explanation.

• Core Idea: The active site is not rigid. It is flexible.
• The active site is initially almost complementary to the substrate.
• When the substrate enters the active site, the binding causes a slight change or 'tweak' in the enzyme's structure. This change is the induced fit.
• This induced change tightens the fit around the substrate, which helps to put strain on the substrate’s bonds, making it easier to break or form new bonds, thus further lowering the activation energy.

Analogy: If Lock-and-Key is like a standard key fitting a rigid lock, Induced-Fit is like putting on a glove. The glove (enzyme) isn't perfectly shaped until your hand (substrate) pushes into it and makes the fabric mold around your fingers.

4. Investigating Enzyme Reactions (3.1.3 & 3.1.4)

A crucial skill in studying enzymes is measuring the rate of reaction. The rate is calculated by monitoring the change in concentration of either the substrate or the product over time.

Measuring Reaction Progress (3.1.3)

We typically measure rate by:

1. Measuring the Rate of Product Formation: We quantify how much product is made per unit time.
   Example: Using the enzyme catalase, which breaks down hydrogen peroxide (\( H_2O_2 \)) into water and oxygen gas (\( O_2 \)). We measure the volume of oxygen gas produced.
2. Measuring the Rate of Substrate Disappearance: We quantify how fast the substrate is used up.
   Example: Using the enzyme amylase, which breaks down starch. We test samples periodically with iodine solution. When the starch disappears, the iodine stops turning blue-black, indicating the end point.

The Role of the Colorimeter (3.1.4)

Sometimes, reactants or products are colored (or produce a colored solution when mixed with an indicator). A colorimeter is a very useful instrument for measuring the concentration of these substances.

• How it works: The colorimeter measures the amount of light absorbed (absorbance) or transmitted (transmission) by a solution.
• During enzyme reactions:
  • If the product is colored (or the substrate disappears), the colorimeter reading changes over time.
  • A higher absorbance usually means a higher concentration of the colored substance.
• By taking regular readings, we can plot a graph and calculate the rate of the enzyme reaction accurately, especially in experiments using amylase (monitoring starch disappearance via iodine test) or invertase (monitoring substrate breakdown).