Table of Contents
Overview: What Makes Enzymes Special?
Enzymes are a particular group of proteins (with a few RNA exceptions) that speed up chemical reactions in cells. In this chapter, the focus is on how their structure (shape and composition) is related to their function (what they do).
You will see that:
- Enzymes have a specific three‑dimensional structure.
- A small region of this structure – the active site – binds the reacting molecule(s).
- The shape and chemical properties of the active site largely explain specificity (which reaction is catalyzed).
- Changes in structure (e.g. by temperature, pH, or mutation) can change or destroy enzyme function.
(How enzyme reactions proceed in time, and how their activity depends on conditions, are covered in the surrounding chapters on enzymatic reactions and enzyme activity.)
Levels of Protein Structure in Enzymes
Enzymes are mostly proteins, and their properties stem from different levels of protein structure. Only key aspects relevant to enzymes are highlighted here.
Primary Structure: Amino Acid Sequence
The primary structure of an enzyme is the linear sequence of amino acids joined by peptide bonds.
- The exact order of amino acids determines:
- which side chains (R‑groups) are present,
- where hydrophobic vs. hydrophilic regions occur,
- which residues can participate directly in catalysis or binding.
A single amino acid change (mutation) can:
- subtly change activity (slower or faster),
- alter which substrate is recognized,
- or completely inactivate the enzyme.
Secondary Structure: Local Folding (α‑Helices and β‑Sheets)
The chain folds locally into α‑helices and β‑pleated sheets, stabilized mainly by hydrogen bonds in the backbone.
In enzymes, secondary structures:
- form stable scaffolds that position important amino acids,
- create binding pockets and channels,
- help define the overall shape of the enzyme.
The catalytic residues are often located at loops connecting helices and sheets, where they are more flexible and accessible.
Tertiary Structure: 3D Shape of a Single Polypeptide
The tertiary structure is the complete three‑dimensional folding of one polypeptide chain. It results from interactions among side chains:
- hydrophobic interactions (hydrophobic residues cluster inside),
- hydrogen bonds,
- ionic interactions (salt bridges),
- disulfide bonds (–S–S–) between cysteines.
For enzymes, tertiary structure is crucial because:
- It shapes the active site (the catalytic pocket).
- It creates channels for substrate entry or product release.
- It allows flexible regions that move during catalysis (induced fit, domain movements).
If tertiary structure is lost (denaturation), the active site is destroyed and the enzyme becomes inactive.
Quaternary Structure: Multi‑Subunit Enzymes
Some enzymes consist of more than one polypeptide chain (subunit). Their quaternary structure is the arrangement of these subunits.
- Each subunit may have its own active site, or
- Multiple subunits may come together to form a composite active site.
Functional implications of quaternary structure:
- Cooperativity: binding of substrate to one subunit can alter the activity of others.
- Regulation: regulatory molecules may bind at interfaces between subunits.
- Stability: multi‑subunit complexes can be more stable and versatile.
Examples include many metabolic enzymes and polymerases (names and details belong to other chapters).
The Active Site: Where Catalysis Happens
The active site is a small, precisely formed region of the enzyme where:
- the substrate(s) bind,
- the chemical transformation takes place.
It is typically composed of:
- a binding region that recognizes and positions the substrate, and
- a catalytic region that carries out the chemical steps.
Substrate Binding: Shape and Chemical Complementarity
Substrate binding depends on:
- Shape complementarity
The three‑dimensional shape of the active site complements the substrate, like a lock and key. But the fit is usually not rigid; see induced fit below. - Chemical complementarity
Noncovalent interactions between enzyme and substrate include: - hydrogen bonds,
- ionic interactions,
- hydrophobic interactions,
- van der Waals forces.
These weak interactions:
- stabilize the enzyme–substrate (ES) complex,
- help exclude water from the active site, which can be important for reaction chemistry,
- position the substrate precisely for the reaction.
Catalytic Residues and Microenvironment
Within the active site, a small number of amino acid side chains directly participate in catalysis. They can:
- donate or accept protons (acid–base catalysis),
- form temporary covalent bonds with the substrate (covalent catalysis),
- stabilize charged transition states (electrostatic catalysis),
- coordinate metal ions (metal ion catalysis).
The enzyme creates a microenvironment:
- Local pH and polarity in the active site can differ from the surrounding solution.
- Water can be partially or wholly excluded.
- Reactive groups are pre‑organized around the substrate.
This microenvironment is a key reason enzymes can achieve very high reaction rates and specificity.
Lock‑and‑Key vs. Induced Fit
Two conceptual models describe enzyme–substrate interaction:
- Lock‑and‑key model
The active site is pre‑formed and fits only one (or a few) substrates. This highlights specificity but ignores flexibility. - Induced fit model
Binding of the substrate induces conformational changes in the enzyme (and sometimes in the substrate). This: - tightens binding after initial contact,
- brings catalytic groups into the perfect geometry,
- helps stabilize the transition state.
In reality, enzymes are dynamic molecules, and induced fit is very common.
Specificity of Enzymes
Enzymes are often highly specific, meaning:
- Substrate specificity: they accept only a particular molecule or a small group of closely related molecules.
- Reaction specificity: they catalyze only one particular chemical transformation (e.g. only hydrolysis of a specific bond).
Specificity arises from:
- detailed 3D structure of the active site,
- arrangement of functional groups that make the correct noncovalent interactions.
Types of specificity include:
- Absolute specificity: one enzyme, one substrate (e.g. an enzyme that acts only on a single sugar).
- Group specificity: enzymes act on a family of related substrates with a common feature (e.g. all compounds with a certain functional group).
- Stereospecificity: enzymes distinguish between mirror‑image forms (D‑ vs L‑isomers) or between different spatial arrangements at a chiral center.
This specificity ensures that cellular metabolism is organized and predictable, with minimal unwanted side reactions.
How Structure Enables Function: Mechanistic Principles
Enzymes do not change the overall energy balance of a reaction (this is handled in thermodynamics‑focused sections). Instead, their structure allows them to change how the reaction proceeds.
Lowering Activation Energy
For a reaction to proceed, reactants must pass through a high‑energy transition state. The activation energy $E_\mathrm{A}$ is the energy barrier between substrates and this state.
Enzymes work by stabilizing the transition state. Structural features that help include:
- precise alignment of substrates,
- creation of temporary bonds and charge distributions,
- exclusion of water and undesired reactions.
Qualitatively, with an enzyme:
- The energy of substrates and products stays the same.
- The peak (transition state) is lower.
- The reaction proceeds faster, in both directions.
Mechanistic Strategies
Several general strategies are used repeatedly by enzymes, enabled by specific structural arrangements:
- Proximity and orientation effects
The active site brings substrates very close and orients them in the correct geometry, increasing the chance of productive collisions. - Acid–base catalysis
Side chains like histidine, aspartate, and glutamate can donate or accept protons, facilitating bond breaking or formation. - Covalent catalysis
The enzyme forms a temporary covalent bond with the substrate (e.g. via serine, cysteine, lysine). This creates a reaction intermediate with a lower energy barrier. - Metal ion catalysis
Bound metal ions (e.g. Zn²⁺, Mg²⁺, Fe²⁺/Fe³⁺) can: - stabilize negative charges,
- help position substrates,
- participate directly in redox reactions.
- Transition state stabilization
The active site often binds the transition state even more tightly than the substrate itself. This selective binding is a major factor in rate enhancement.
Which strategies are used depends on the enzyme’s precise structural arrangement.
Cofactors and Coenzymes
Some enzymes require additional non‑protein components to function. These components are closely integrated into the enzyme’s structure and essential for its function.
Types of Cofactors
- Inorganic cofactors (metal ions)
Examples: Mg²⁺, Zn²⁺, Fe²⁺/Fe³⁺, Cu²⁺, Mn²⁺.
Roles: - stabilize charges,
- bind substrates (e.g. ATP binds with Mg²⁺),
- participate in electron transfer.
- Organic cofactors (coenzymes)
Small organic molecules, often derived from vitamins (e.g. NAD⁺ from niacin, FAD from riboflavin).
Roles: - transfer specific atoms or groups (e.g. electrons, acyl groups),
- participate in redox reactions or group transfer.
Apoenzyme, Holoenzyme, and Prosthetic Groups
- Apoenzyme: the protein part of the enzyme without its cofactor; usually inactive.
- Holoenzyme: the complete, active form including its necessary cofactors.
Some cofactors are:
- Loosely bound (typical for many coenzymes):
- They may diffuse in and out of the active site.
- They are regenerated in other reactions.
- Tightly or covalently bound (prosthetic groups):
- Permanently associated with the enzyme.
- Integral to the structure and function (e.g. heme groups in some oxidoreductases).
Thus, full understanding of an enzyme’s function includes both its protein structure and any associated cofactors.
Allosteric Sites and Structural Regulation (Overview)
Beyond the active site, many enzymes possess additional binding sites that are not directly involved in catalysis but influence it.
- These are called allosteric sites.
- Binding of regulatory molecules here causes conformational changes that:
- increase activity (allosteric activation), or
- decrease activity (allosteric inhibition).
Key points about allosteric regulation tied to structure:
- It often involves multi‑subunit (quaternary) enzymes.
- Structural changes can propagate from one subunit to another.
- The enzyme may exist in different conformational states (e.g. “active” vs. “less active”), shifted by ligand binding.
Detailed treatment of enzyme regulation and activity is given in the dedicated chapter, but the structural basis lies in the enzyme’s ability to change shape in response to ligand binding.
Structural Stability and Denaturation
The delicate three‑dimensional structure of enzymes depends on many weak interactions. Under unfavorable conditions, these interactions can be disrupted:
- High temperatures can increase molecular motion and break noncovalent interactions, leading to loss of structure (denaturation).
- Extreme pH can change the charge state of side chains, disrupting ionic bonds and hydrogen bonds.
- Organic solvents or detergents can disturb hydrophobic interactions.
When denaturation occurs:
- secondary, tertiary, and quaternary structures are altered or lost,
- the active site is distorted or destroyed,
- the enzyme typically loses its catalytic function.
If only mild changes occur, some enzymes can refold when normal conditions are restored, but often denaturation is effectively irreversible in cells.
Enzyme Classification and Structure (Brief Orientation)
Enzymes are classified based on the type of reaction they catalyze (oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases). While classification is covered elsewhere, there is a structural angle:
- Different enzyme classes often share common structural motifs or domains suited to their type of chemistry.
- Closely related enzymes (e.g. within a family) may have:
- similar overall folds,
- similarly arranged active‑site residues,
- but different side chains in the binding pocket, giving different substrate specificities.
Thus, small structural variations can create entire families of enzymes with related but distinct functions.
Summary
- Enzymes are mainly proteins whose three‑dimensional structure determines their function.
- The active site is formed by a small set of key residues positioned by the overall fold; it binds substrates and stabilizes the transition state.
- Enzyme specificity (which substrate and which reaction) follows from precise shape and chemical complementarity in the active site.
- Structural features enable catalytic strategies such as acid–base catalysis, covalent catalysis, metal ion catalysis, and transition state stabilization.
- Many enzymes rely on cofactors (metal ions) or coenzymes (organic molecules) as part of their functional structure.
- Allosteric sites and multi‑subunit organization allow regulation through conformational changes.
- Disruption of structure (denaturation) usually destroys function, highlighting the intimate link between enzyme structure and enzyme function.