Biology | Enzymes and metabolism

Welcome to Enzymes and Metabolism!

Hello future biologist! This chapter, Enzymes and Metabolism, is absolutely fundamental. It sits squarely in the "Interaction and Interdependence" section of the course because enzymes are the ultimate managers, controlling every single chemical interaction within a living cell.

If you can understand how these amazing protein machines work, you'll unlock the secrets to cellular life, energy processing (like cell respiration and photosynthesis), and even how medicines work. Don't worry if it seems complex at first; we will break it down into manageable steps!

1. Enzymes: The Catalysts of Life

What Exactly is an Enzyme?

Think of life as a massive, continuous factory floor running thousands of chemical reactions every second. These reactions need managers to ensure they happen fast enough to support life. That manager is the enzyme.

• Definition: An enzyme is a biological catalyst, usually a protein, that speeds up a specific chemical reaction without being used up itself.
• Key Fact: Enzymes only affect the rate of a reaction; they do not change the final products or the overall energy released or consumed.
• Reusability: Since they are unchanged by the reaction, enzymes can be used over and over again—very efficient!

The Role of Activation Energy

Every chemical reaction needs a little bit of a "push" to get started. This initial energy barrier is called the activation energy (\(E_a\)).

Analogy: Imagine pushing a heavy boulder up a hill. Once it reaches the top, it rolls down the other side easily (forming the product). The height of the hill is the activation energy.

• Enzymes work by lowering the activation energy.
• In our analogy, the enzyme digs a tunnel straight through the hill, requiring much less effort (energy) to get the reaction going quickly.

2. How Enzymes Interact: Specificity and the Active Site

The Lock-and-Key vs. Induced-Fit Models

Enzymes are highly specific. A digestive enzyme like lipase only breaks down lipids; it won't touch starch. This specificity is determined by structure.

The enzyme acts on a molecule called the substrate.

1. The substrate binds to a specific region on the enzyme called the active site.
2. Once bound, they form an Enzyme-Substrate Complex (ESC).
3. The reaction occurs, products are released, and the enzyme is ready for the next substrate.

Model 1: The Lock-and-Key Hypothesis (Simple)

The active site (the lock) has a shape perfectly complementary to the substrate (the key). This model explains specificity well, but it's a bit rigid.

Model 2: The Induced-Fit Model (More Accurate)

This is the model IB prefers you to understand deeply.

When the substrate approaches the enzyme, the active site is not a perfect fit. Instead, the active site changes its shape slightly to precisely wrap around the substrate.

Analogy: Think of the enzyme as a glove and the substrate as your hand. The glove isn't rigid; it changes shape slightly to fit the contours of your hand better when you put it on. This tight, induced fit maximizes the catalytic efficiency.

Key Takeaway: The active site of an enzyme is complementary to the substrate, and this complementary fit is enhanced by conformational changes known as induced fit.

3. Factors Affecting Enzyme Activity

Since enzymes are proteins, their complex 3D shape (conformation) is vital to their function. Anything that disrupts this shape will reduce or stop enzyme activity.

A. Temperature

• Low Temperatures: Enzyme activity is slow. Molecules move slowly, resulting in fewer collisions between the enzyme and substrate (low kinetic energy). The enzyme structure is intact, but the reaction rate is low.
• Optimum Temperature: The temperature at which the enzyme works fastest (e.g., typically around 37°C in humans). Kinetic energy is high, maximizing collisions.
• High Temperatures: Activity drops sharply above the optimum. High heat breaks the weak bonds (like hydrogen bonds) maintaining the enzyme's 3D structure. The active site loses its shape—this is called denaturation.
• Important Point: Denaturation is usually irreversible. Once an egg is cooked (denatured), you can't "uncook" it!

B. pH (Acidity/Alkalinity)

• Each enzyme has an optimum pH.
• Deviations from the optimum pH disrupt the ionic and hydrogen bonds holding the tertiary structure of the protein together.
• Example: Pepsin (in the stomach) has an optimum pH of about 2 (highly acidic). Amylase (in saliva) has an optimum pH of about 7 (neutral). If you put pepsin in a neutral solution, it would barely function.

C. Substrate Concentration

• As substrate concentration increases, the rate of reaction increases because there are more frequent collisions with the active sites.
• However, the rate eventually levels off and reaches a maximum velocity (\(V_{max}\)).
• Limiting Factor: At \(V_{max}\), the enzyme is saturated—all active sites are constantly occupied. To increase the rate further, you would need to add more enzyme.

4. Metabolism: The Sum of Chemical Interactions

What is Metabolism?

Metabolism is the entire collection of all enzyme-catalyzed reactions that occur within an organism. These reactions are often organized into chains or cycles called metabolic pathways.

Enzymes ensure that these pathways are followed precisely, without wasteful side reactions.

Metabolism is broadly divided into two main categories:

A. Anabolism (Building Up)

• Definition: Reactions that synthesize larger, more complex molecules from smaller ones.
• Energy Requirement: Anabolic reactions require energy input (they are endergonic).
• Example: Building proteins from amino acids (Protein synthesis), or building starch/glycogen from glucose.

B. Catabolism (Breaking Down)

• Definition: Reactions that break down large molecules into smaller, simpler ones.
• Energy Requirement: Catabolic reactions release energy (they are exergonic), often stored as ATP.
• Example: Digestion of food, or Cell Respiration (breaking down glucose to release energy).

Did you know? Anabolism and Catabolism are tightly interdependent. Catabolism provides the energy (ATP) needed to fuel Anabolism, ensuring the cell remains in balance.

5. Controlling the Pathway: Enzyme Inhibition (Regulation)

Cells don't just run reactions randomly; they control them precisely based on their needs. This control is achieved through regulating enzyme activity, primarily using inhibitors.

A. Competitive Inhibition

A competitive inhibitor is a molecule that closely resembles the substrate. It competes directly with the substrate for the active site.

• Mechanism: The inhibitor binds to the active site, preventing the substrate from binding.
• Overcoming Inhibition: This type of inhibition can be overcome by increasing the substrate concentration. If there are vastly more substrates than inhibitors, the substrates are more likely to successfully reach the active site first.
• Analogy: A rival key that fits the lock (active site) just well enough to block your key (substrate).

B. Non-Competitive Inhibition (Allosteric Control)

A non-competitive inhibitor (or allosteric inhibitor) does NOT bind to the active site.

• Mechanism: It binds to a different site on the enzyme called the allosteric site.
• When the inhibitor binds to the allosteric site, it causes a conformational change (a change in shape) in the entire enzyme, including the active site.
• This structural change means the active site can no longer bind the substrate effectively, or catalyze the reaction.
• Overcoming Inhibition: Increasing substrate concentration has no effect because the active site shape is permanently altered (as long as the inhibitor is bound).

C. Common Mistakes to Avoid

DO NOT say: "The enzyme is destroyed during the reaction."
DO SAY: "The enzyme is reusable; it is unchanged by the reaction."

DO NOT confuse: Denaturation and inhibition. Denaturation is a permanent structural loss due to heat/pH. Inhibition is a reversible (or sometimes irreversible) blockage of the active site by a chemical molecule.

Final Key Takeaway: Enzymes are central to life, managing the speed and direction of metabolism (anabolism and catabolism) and ensuring efficient interactions within the cell. The ability to regulate these enzymes through inhibition allows the cell to respond dynamically to changing needs.