Chapter 6: Enzymes – The Catalysts of Life (Cell Biology Study Notes)

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Enzymes: The Catalysts of Life

Introduction to Enzyme Catalysis

Enzymes are biological catalysts, primarily proteins, that accelerate nearly all cellular chemical reactions. The presence of the appropriate enzyme determines whether a reaction will occur under cellular conditions.

Enzyme catalysis: Nearly all cellular reactions require enzymes to proceed at appreciable rates.
Key role: Enzymes make the difference between a reaction being possible and actually occurring in the cell.

Activation Energy and the Metastable State

Thermodynamics and Reaction Rates

Many reactions are thermodynamically feasible but do not occur rapidly due to energy barriers. For example, ATP hydrolysis is energetically favorable but ATP remains stable in water for days.

Example reaction: ATP + H2O → ADP + Pi
Free energy change:

Activation Energy Barrier

Before a chemical reaction can occur, reactants must overcome the activation energy barrier.

Activation energy (): Minimum energy required for reactants to collide and form products.
Transition state: An intermediate stage with higher free energy than reactants.

Graphical Representation

The following graph illustrates the energy changes during an uncatalyzed reaction:

Transition state: Peak of the energy curve.
: Energy difference between reactants and transition state.
: Overall free energy change.

Catalysts and Activation Energy

Catalysts enable reactions by lowering the activation energy () barrier, either by increasing molecular energy or by providing a surface for reactants to interact.

Isothermal systems: Cells maintain constant temperature, so increasing heat is not practical.
Catalysts: Lower and remain unchanged after the reaction.

Enzymes as Biological Catalysts

Properties of Catalysts

Increase reaction rates by lowering .
Form transient, reversible complexes with substrates.
Change the rate at which equilibrium is achieved, not the position of equilibrium.

Organic catalysts in cells are called enzymes.

Enzyme Structure and Active Site

Most enzymes are proteins; some RNA molecules (ribozymes) also have catalytic activity.
The active site is a specific cluster of amino acids formed by protein folding, where substrates bind and catalysis occurs.
Active sites are typically grooves or pockets with high substrate affinity.

Amino Acids in Active Sites

Only a few amino acids are commonly involved: cysteine, histidine, serine, aspartate, glutamate, lysine.
These amino acids can bind substrates and act as proton donors/acceptors.

Cofactors and Prosthetic Groups

Some enzymes require non-protein cofactors for activity, often as electron acceptors.
Prosthetic groups: Metal ions or small organic molecules (coenzymes, often vitamin derivatives) essential for enzyme function.
Example: Catalase contains a porphyrin ring with an iron atom.

Enzyme Specificity and Classification

Substrate and Group Specificity

Enzymes exhibit high substrate specificity due to the shape and chemistry of the active site.
Group specificity: Some enzymes act on a group of related substrates, common in polymer degradation.

Enzyme Diversity and Nomenclature

Enzymes are named based on substrate (e.g., protease, amylase) or function (e.g., trypsin, catalase).
The Enzyme Commission (EC) classifies enzymes into six major classes:

Class	Reaction Type	Example	Reaction Catalyzed
Oxidoreductases	Oxidation-reduction reactions; electron transfer	Alcohol dehydrogenase	Oxidation of ethanol to acetaldehyde as NAD+ is reduced to NADH
Transferases	Transfer of functional groups from one molecule to another	Hexokinase	Phosphorylation of glucose to glucose-6-phosphate using ATP
Hydrolases	Hydrolytic cleavage of molecules into two products	Glucose-6-phosphatase	Cleavage of phosphate group from ATP
Lyases	Removal or addition of a group to a molecule	Aldolase	Removal of a carbon fragment from fructose-1,6-bisphosphate
Isomerases	Movement of a functional group within a molecule	Malate isomerase	Conversion of malate to fumarate
Ligases	Joining of two molecules into one	Pyruvate carboxylase	Addition of CO2 to pyruvate to produce oxaloacetate

Enzyme Sensitivity to Environmental Factors

Temperature Sensitivity

Enzyme activity increases with temperature due to increased kinetic energy, but excessive heat causes denaturation and loss of activity.
Optimal temperature for human enzymes: 37°C.
Most homeotherm enzymes are inactivated above 50–55°C.
Some enzymes are sensitive at 40°C; others (e.g., archaea) function at high temperatures; cryophilic enzymes (e.g., Listeria) work at low temperatures.

pH Sensitivity

Most enzymes are active within a pH range of 3–4 units.
pH affects the charge of amino acids at the active site, influencing ionic and hydrogen bonds.
Example: Pepsin optimum at pH ~2 (stomach); trypsin optimum at pH ~8 (intestine).

Sensitivity to Other Factors

Enzymes are affected by inhibitors, activators, and ionic strength, which influence tertiary structure and activity.

Substrate Binding, Activation, and Catalysis

Substrate Binding

Substrates bind to the active site via hydrogen and ionic bonds, in the correct orientation for reaction.
Binding is readily reversible.

Induced-Fit Model

Unlike the rigid lock-and-key model, the induced-fit model describes the enzyme as flexible, changing shape upon substrate binding.
Conformational change brings necessary amino acid side chains into the active site for catalysis.

Substrate Activation Mechanisms

Bond distortion: Weakens substrate bonds for easier catalytic attack.
Proton transfer: Increases substrate reactivity.
Electron transfer: Forms temporary covalent bonds between enzyme and substrate.

The Catalytic Event Sequence

Random collision of substrate with active site leads to binding.
Binding induces conformational change, facilitating conversion to products.
Products are released from the active site.
Enzyme returns to original conformation, ready for another substrate.

Ribozymes: Catalytic RNA Molecules

Discovery and Examples

Ribozymes are RNA molecules with catalytic activity, discovered in the 1980s.
Examples: Tetrahymena RNA (self-splicing, autocatalysis), Ribonuclease P (RNA component cleaves tRNA precursors), Ribosomal RNA (peptidyl transferase activity).

Enzyme Inhibition

Types of Inhibitors

Enzymes are inhibited by products, alternative substrates, substrate analogues, drugs, toxins, and allosteric effectors.
Inhibition is a vital cellular control mechanism; many drugs and poisons act by inhibiting enzymes.

Important Inhibitors

Substrate analogues: Resemble real substrates, occupy active site but do not react; useful in fighting infectious diseases.
Transition state analogues: Mimic transition state, block enzyme activity.

Irreversible vs. Reversible Inhibition

Irreversible inhibitors: Bind covalently, permanently inactivating the enzyme (e.g., heavy metals, nerve gas).
Reversible inhibitors: Bind noncovalently, can dissociate; fraction of active enzyme depends on inhibitor concentration.

Equation for reversible inhibition:

Types of Reversible Inhibitors

Competitive inhibitors: Bind the active site, compete with substrate, directly inhibit activity.
Noncompetitive inhibitors: Bind elsewhere, cause conformational change, indirectly inhibit activity.

Enzyme Regulation

Substrate-Level Regulation

Enzyme rates are adjusted by substrate and product concentrations.
Increased substrate increases reaction rate; increased product decreases rate.

Allosteric Regulation and Covalent Modification

Enzymes can be regulated by molecules binding at sites other than the active site (allosteric regulation) or by addition/removal of chemical groups (covalent modification).
Allosteric enzymes have two conformations: high-affinity (active) and low-affinity (inactive).
Allosteric effectors (activators or inhibitors) bind to the regulatory site, shifting equilibrium between conformations.

Feedback Inhibition

End-product of a pathway inhibits an earlier step, preventing overproduction.

Covalent Modification

Enzyme activity can be regulated by phosphorylation (addition of phosphate group) or dephosphorylation (removal of phosphate group).
Protein kinases: Catalyze phosphorylation, usually using ATP.
Protein phosphatases: Catalyze dephosphorylation.
Phosphorylation can activate or inhibit enzymes, depending on the context.