Table of Contents
Overview: What Happens During an Enzyme-Catalyzed Reaction?
In this chapter, we follow the sequence of events in an enzymatic reaction from the first collision of substrate and enzyme to the release of products. We focus on the course (the step-by-step process), not on enzyme structure or on how activity is regulated (covered in other chapters).
Many details can be summarized in a general reaction scheme:
$$
\text{E} + \text{S} \;\rightleftharpoons\; \text{ES} \;\rightleftharpoons\; \text{EP} \;\rightleftharpoons\; \text{E} + \text{P}
$$
- $E$ = enzyme
- $S$ = substrate
- $ES$ = enzyme–substrate complex
- $EP$ = enzyme–product complex
- $P$ = product(s)
Not every enzyme goes through all formally separable stages, but this scheme helps describe the typical course of many enzymatic reactions.
1. Encounter and Binding: Formation of the Enzyme–Substrate Complex
1.1 Random molecular collisions
In aqueous solution, all molecules constantly move and collide with each other due to Brownian motion. The first prerequisite for a reaction is that substrate and enzyme must meet.
- The rate of encounter depends on the concentrations of enzyme and substrate and on diffusion.
- Most collisions do not lead to binding or reaction; the molecules must also fit together chemically and spatially.
1.2 Binding at the active site
When a substrate molecule collides with an enzyme, it may bind to a specific region, the active site.
Two classical models describe how binding can be viewed:
- Lock-and-key model:
The active site has a preformed shape complementary to the substrate. Binding is like inserting a key into a lock. - Induced-fit model:
The active site is flexible. Binding of the substrate causes a slight change in the shape of the enzyme so that the fit becomes better.
Today, the induced-fit idea is considered more realistic for most enzymes. It explains why many enzymes:
- Distinguish very similar substrates (high specificity).
- Become catalytically competent only after substrate binding (binding helps organize the active site).
1.3 Reversible binding
The initial binding step is usually reversible:
$$
\text{E} + \text{S} \;\rightleftharpoons\; \text{ES}
$$
- Substrate binds and unbinds many times before a reaction actually occurs.
- The enzyme–substrate complex (ES) is a central intermediate: enzyme and substrate are associated, but the substrate has not yet been fully converted into product.
The stability of ES is determined by many weak interactions (e.g., hydrogen bonds, ionic interactions, hydrophobic interactions, van der Waals forces).
2. Lowering the Activation Energy: Transition State and Catalysis
2.1 Activation energy and transition state
Even if a reaction is energetically favorable overall (negative change in free energy, $\Delta G < 0$), it usually does not occur spontaneously at a significant rate, because reactants must first pass through a high-energy intermediate state: the transition state.
- The activation energy $E_\text{A}$ is the energy needed to reach the transition state.
- Without a catalyst, this barrier is often too high for many reactions to occur rapidly in cells.
Enzymes do not change the overall energy difference between substrate and product ($\Delta G$), but they lower $E_\text{A}$, making the reaction faster.
2.2 The enzyme–substrate complex and the transition state
Within the ES complex, the substrate is brought into a transition-state-like configuration. The enzyme stabilizes this normally very unstable form and thereby lowers the activation energy.
This is often represented as:
$$
\text{ES} \;\rightarrow\; \text{E}^{\ddagger}\text{S}^{\ddagger} \;\rightarrow\; \text{EP}
$$
- The ‡ (double dagger) symbol denotes the transition state.
- The enzyme binds the substrate not optimally as substrate, but especially well in a configuration close to the transition state. This is crucial for catalysis.
2.3 Mechanisms by which enzymes accelerate reactions
During the course of the reaction, enzymes use several general strategies (often in combination):
- Proximity and orientation effects
- Reactants are brought close together and in the correct orientation.
- This increases the probability of bond formation or breakage.
- Acid–base catalysis
- Certain amino acid side chains in the active site act as proton donors (acids) or proton acceptors (bases).
- This can facilitate bond cleavage or the formation of new bonds.
- Covalent catalysis
- A transient covalent bond is formed between the enzyme and the substrate.
- The enzyme temporarily becomes part of the substrate, forming an enzyme–substrate intermediate that is more reactive than the free substrate.
- Metal ion catalysis
- Metal ions (e.g., Zn²⁺, Mg²⁺, Fe²⁺/Fe³⁺) can participate in catalysis by:
- Stabilizing negative charges,
- Facilitating redox (electron transfer) reactions, or
- Helping correctly orient the substrate.
- Strain and distortion
- Binding can slightly distort the substrate, forcing it into a geometrically strained configuration closer to the transition state.
Which of these mechanisms is used depends on the specific enzyme and reaction.
3. Chemical Transformation: From Substrate to Product
After the transition state is reached, the actual chemical transformation occurs:
- Bonds are broken (e.g., hydrolysis of a peptide bond).
- New bonds are formed (e.g., formation of new covalent connections between fragments).
- Electrons, protons, or small groups may be transferred.
In the simplified notation:
$$
\text{ES} \;\rightleftharpoons\; \text{EP}
$$
- The ES complex transitions into an enzyme–product complex (EP).
- The enzyme ensures that, from the favored transition state, product formation is more probable than return to substrate.
For many reactions, this step is essentially irreversible under physiological conditions, particularly if product is rapidly removed or further metabolized in subsequent reactions.
4. Product Release and Enzyme Recovery
4.1 Dissociation of product
Once the substrate has been converted, the binding affinity of the product for the active site is usually lower than that of the substrate or the transition state:
$$
\text{EP} \;\rightleftharpoons\; \text{E} + \text{P}
$$
- The product detaches from the enzyme and diffuses away.
- The enzyme is now free again and can bind another substrate molecule.
4.2 Enzyme remains chemically unchanged
A fundamental feature of enzymes as catalysts:
- At the end of the reaction cycle, the enzyme is regenerated in its original form.
- It emerges chemically unchanged, ready for another catalytic cycle.
- A single enzyme molecule can thus convert many substrate molecules per unit time.
This turnover rate (number of substrate molecules converted per unit time per enzyme molecule) is part of what is measured when determining enzyme activity (explored in a later chapter).
5. Multi-Step Reactions and Complex Courses
Not all reactions are simple one-step conversions of one substrate to one product. The course of more complex enzymatic reactions typically involves several related features.
5.1 Reactions with multiple substrates
Many enzymes act on two or more substrates (e.g., kinases transfer a phosphate from ATP to another molecule). Typical schemes include:
- Sequential (single-displacement) mechanisms
- All substrates must bind before any product is released.
- Ordered: one substrate always binds first (e.g., $E + A \rightarrow EA; EA + B \rightarrow EAB; \dots$).
- Random: substrates can bind in any order.
- Ping-pong (double-displacement) mechanisms
- One substrate binds and a product is released before the second substrate binds.
- The enzyme alternates between different forms (e.g., $E \rightarrow E' \rightarrow E$), often carrying a transferred group in the intermediate state.
Although mechanistically diverse, the course still follows the same basic pattern: binding → transformation(s) → product release → recovery of the active form of the enzyme.
5.2 Reaction pathways and enzyme complexes
In living cells, products of one enzyme reaction are often immediately used as substrates for another:
- Sometimes several enzymes form multi-enzyme complexes.
- Intermediates are passed directly from one active site to the next (often called substrate channeling).
- This can:
- Increase the overall speed of the pathway.
- Prevent loss or unwanted side reactions of intermediates.
- Allow precise spatial and temporal control of the reaction sequence.
Again, each individual enzymatic step follows the same fundamental course, but multiple steps are tightly linked.
6. Energetics and Direction of the Reaction
6.1 Equilibrium and direction
Enzymes accelerate both the forward and reverse reactions because they lower the activation energy for both directions:
- They do not change the position of the chemical equilibrium.
- They only change how quickly the equilibrium is reached.
The direction in which a reaction runs in the cell depends on:
- The relative concentrations of substrates and products.
- The overall free energy change ($\Delta G$) under physiological conditions.
- Coupling to other reactions (for example, using the free energy of ATP hydrolysis).
6.2 Coupling of reactions
Many endergonic (energy-requiring) reactions are made possible in metabolism by coupling them to exergonic (energy-releasing) reactions, often via enzymes:
- Enzymes can bind and process both types of reactants in a single catalytic cycle, so that energetically unfavorable partial reactions proceed because they are linked to favorable ones.
- The course of such coupled reactions is still: binding → formation of a complex → transition state → products + regenerated enzyme, but now involving more than one chemical transformation.
7. Summary of the Course of an Enzymatic Reaction
The essential stages, abstracted from any specific example, are:
- Encounter:
Enzyme and substrate collide due to molecular motion. - Binding:
Substrate binds reversibly to the active site, forming the enzyme–substrate complex (ES). The active site may adjust (induced fit). - Formation of the transition state:
Within ES, the enzyme stabilizes a transition-state-like configuration and thereby lowers the activation energy. - Chemical conversion:
Bonds are broken and formed; the substrate is transformed into product, often through defined intermediates (ES → EP). - Product release:
Product dissociates from the enzyme (EP → E + P). - Enzyme regeneration:
The enzyme is chemically unchanged and ready to begin another catalytic cycle.
Understanding this general course is the basis for analyzing how enzymes work in detail and for interpreting how temperature, pH, concentration, and regulatory mechanisms (treated in related chapters) affect enzyme-catalyzed reactions in living organisms.