Unit 1: 3.1.3 Biochemical reactions in cells are controlled by enzymes

Hello Biologists! This chapter is incredibly important. Enzymes are the invisible workforce inside every single cell, making life possible. If they stop working, your cell stops working! We will explore exactly how these vital molecules speed up reactions and what keeps them running smoothly.

3.1.3.1 Enzymes and enzyme action

What exactly are Enzymes?

Enzymes are special types of proteins that act as biological catalysts.

  • A catalyst is a substance that speeds up a chemical reaction without being used up itself.
  • Since enzymes are proteins, their structure—especially the complex tertiary structure (their 3D shape)—is essential for their function. If the shape changes, the enzyme cannot work.
The Role of Enzymes: Lowering Activation Energy

Every chemical reaction needs a little 'push' to get started. This initial energy input is called the activation energy.

Think of it like this: You want to push a heavy boulder over a hill. The effort you need to get it to the top is the activation energy. Once over the top, it rolls down easily.

An enzyme acts by creating a detour, lowering the height of the hill (the activation energy). This means the reaction can happen much faster and under cellular conditions (like normal body temperature).

How Enzymes Interact with Substrates

Enzymes work by binding to the molecule they are meant to change. This molecule is called the substrate.

The specific region on the enzyme where the substrate binds is called the active site.

When the substrate slots perfectly into the active site, they form a temporary structure known as the enzyme-substrate complex (ESC).

  • Formation of the ESC allows the enzyme to hold the substrate molecules in a way that speeds up bond breaking or formation, lowering the activation energy.
  • The enzyme then releases the products, and the active site is ready to bind to another substrate molecule.
Models of Enzyme Action

Our understanding of how enzymes work has developed over time:

1. The Lock and Key Model (Older Idea)

This model suggests that the substrate (the key) has a complementary shape that fits perfectly and rigidly into the active site (the lock).

Limitation: This model explains enzyme specificity well, but it doesn't explain how the enzyme actually stresses the bonds in the substrate to speed up the reaction.

2. The Induced Fit Model (Current Accepted Model)

The active site is not completely rigid. While the substrate must be roughly complementary, the active site changes shape slightly to fit the substrate more precisely once binding begins.

Analogy: Think of fitting your hand into a high-quality leather glove. The glove (active site) isn't exactly the shape of your hand until you put your hand in, then it molds perfectly around it.

Why Induced Fit is better:

  • This slight shift in the enzyme shape puts strain on the bonds within the substrate molecule, making it much easier for the reaction to occur (further lowering the activation energy).

Key Takeaway 3.1.3.1: Enzymes are protein catalysts that lower the activation energy needed for reactions. They bind to the substrate at the active site, forming an enzyme-substrate complex. The induced fit model explains how the active site adjusts its shape slightly to achieve the perfect reaction-catalysing complex.

3.1.3.2 The properties of enzymes

Enzyme Specificity

Enzymes are highly specific in their action.

  • The shape of the active site is determined by the enzyme’s tertiary structure, which is unique to each type of enzyme.
  • Only one specific type of substrate molecule will have the complementary shape required to fit into that active site, ensuring that only the correct biological reactions occur in the cell.

Did you know? Enzymes are named by adding '-ase' to the substrate they act upon. E.g., Lipase digests lipids, Protease digests proteins, and Lactase digests lactose.

Factors Affecting the Rate of Enzyme-Controlled Reactions

The speed of an enzyme reaction depends on two main things:

  1. How often the enzyme and substrate collide (collision frequency).
  2. Whether the active site can successfully bind to the substrate (complementarity/shape).

Let's look at the factors that influence these rates:

1. Temperature

Temperature affects both collision frequency and the ability of the active site to bind.

  • Low Temperature: Molecules (both enzyme and substrate) have low kinetic energy, so they move slowly. This results in fewer successful collisions, and the reaction rate is slow.
  • Optimum Temperature: This is the temperature at which the reaction rate is highest (usually around 37 °C in humans). Kinetic energy is high, resulting in maximum collisions.
  • High Temperature (Above Optimum): Increasing temperature causes intense vibrations within the enzyme structure. These vibrations break the weak bonds (like hydrogen and ionic bonds) that maintain the specific tertiary structure of the active site.

When the active site permanently loses its specific shape, the enzyme is denatured. The substrate can no longer bind, and the reaction stops. Denaturation is usually irreversible.

2. pH

pH measures the concentration of hydrogen ions (\(H^+\)). pH affects the charges on the amino acids (R-groups) found in the active site.

  • Optimum pH: The specific pH where the enzyme's active site has the correct charge distribution and shape for maximum binding (e.g., pH 2 for stomach enzyme Pepsin, but pH 7 for salivary amylase).
  • Deviation from Optimum: If the environment becomes too acidic or too alkaline, the \(H^+\) ions interfere with the charges on the R-groups, breaking the ionic bonds that hold the tertiary structure together.

This results in a change in the active site shape and denaturation, drastically reducing the rate of reaction.

3. Substrate Concentration

If the enzyme concentration is constant, the rate of reaction increases as the substrate concentration increases.

  • More substrate molecules mean a higher probability of successful collisions with the active sites.
  • However, the rate eventually levels off and reaches a plateau. Why? Because all the active sites are currently occupied. The enzymes are saturated, and the enzyme concentration becomes the limiting factor.
4. Enzyme Concentration

If the substrate concentration is kept high (non-limiting), increasing the enzyme concentration linearly increases the rate of reaction.

  • More enzyme molecules mean more available active sites.
  • This leads to the formation of more enzyme-substrate complexes per unit of time.
5. Competitive and Non-Competitive Inhibitors

Inhibitors are molecules that slow down or stop enzyme reactions. They affect the ability of the active site to bind to the substrate. Don't worry if this seems tricky at first, the distinction is mainly about where they bind.

a) Competitive Inhibitors
  • Action: These inhibitors have a similar shape to the substrate and compete directly with the substrate to enter the active site.
  • Effect: They block the active site temporarily.
  • Reversal: If you increase the substrate concentration, the substrate molecules are more likely to collide with the active site than the inhibitor, overcoming the inhibition.

Think of competitive inhibition as musical chairs: both the substrate and inhibitor are fighting for the same seat (the active site).

b) Non-Competitive Inhibitors
  • Action: These inhibitors bind to a site on the enzyme that is not the active site, often called the allosteric site.
  • Effect: Binding to the allosteric site causes the enzyme's entire 3D shape, including the active site, to change shape permanently (or semi-permanently).
  • Reversal: Increasing the substrate concentration will not reverse the effect because the active site shape has been fundamentally altered and is no longer complementary, regardless of how many substrates are available.

Quick Review of Rate Factors:

  • Temperature and pH influence the enzyme's 3D structure; extreme values cause denaturation.
  • Concentrations (S and E) determine the frequency of successful collisions.
  • Inhibitors block the enzyme; competitive ones fight for the active site, non-competitive ones change the active site's shape by binding elsewhere.