Enzyme structure, function and activity

Enzyme structure and function

Enzymes are specialized proteins that act as biological catalysts, greatly accelerating chemical reactions in living organisms by lowering the activation energy. In doing so, they facilitate vital processes such as the following, all at temperatures and pH levels compatible with cellular life:

• Metabolism
• DNA synthesis
• RNA synthesis
• Protein synthesis
• Digestion

Enzymes DO:

• …increase the rate constant, $k$, for the equation rate = $k[A][B]$
• .…speed up both forward and reverse reactions
• …affect a reaction’s kinetics, but not the thermodynamics.

Enzymes DO NOT:

• …alter the $K_{eq}$ of a reaction (because lowers activation energy for forward/reverse)
• …change $\Delta$$G$, the net change in free energy

Composition

• Enzymes are composed of either protein, as in the vast majority of enzymes in the human body, or RNA, with the most important human RNA-based enzyme being the ribosome.

Classification by reaction type

Enzymes are often grouped according to the type of reaction they catalyze. Examples include

• Oxidoreductases, which handle redox transformations
• Transferases, which relocate functional groups
• Hydrolases, which cleave bonds using water
• Lyases, which break bonds without hydrolysis or oxidation
• Isomerases, which rearrange molecular structures
• Ligases, which form new bonds, typically driven by ATP.

Substrates and specificity

Each enzyme selectively binds one or more substrates—the molecules undergoing reaction—based on a precise three-dimensional complementarity. This specificity stems from structural compatibility between the substrate and the enzyme’s active site, promoting the correct alignment and efficient chemical conversion. Enzymes typically exhibit high specificity, recognizing subtle differences in substrate shape or functional groups, even as specifically as differentiating stereoisomers.

Mechanism of catalysis and role of cofactors

Enzymes employ diverse strategies to facilitate reactions:

• They may physically bring substrates into close proximity, stabilize charged intermediates, or distort bonds to mimic the reaction’s transition state. Some require cofactors or coenzymes—non-protein entities that assist in catalysis.
• Cofactors can be metal ions (e.g., zinc, iron), while coenzymes are often carbon-based molecules such as vitamins or their derivatives. Lock and key model: rigid active site.
• The water-soluble vitamins (e.g., B-complex vitamins) frequently act as coenzyme precursors, forming essential components like NAD⁺ or FAD.
• These auxiliary players help shuttle electrons or chemical groups, enabling reactions that the enzyme’s amino acid side chains cannot perform on their own.

Effects of local conditions

Enzyme activity can be profoundly influenced by environmental factors such as pH, temperature, and concentrations of substrates or products. Each enzyme operates optimally within a specific pH range and temperature window.

Deviations can impair hydrogen bonding or disrupt the protein’s folding, leading to decreased activity or denaturation.

In cells, compartmentalization and regulatory molecules further refine these conditions, ensuring enzymes function at the proper pace and location.

Control of enzyme activity

Enzyme activity is governed by a variety of mechanisms that fine-tune how rapidly a catalyzed reaction proceeds, ensuring cells can adapt to changing conditions.

One key area of study is kinetics, which investigates how reaction rates respond to shifts in substrate concentration, enzyme concentration, and other factors. A classic model used to describe these relationships is the Michaelis–Menten framework, which characterizes how an enzyme’s velocity evolves with increasing substrate levels until reaching a maximum rate.

Certain enzymes exhibit cooperativity, meaning the binding of a substrate to one subunit or site affects the affinity of other subunits or sites, producing a more dynamic response curve.

Feedback regulation

Beyond these intrinsic kinetic properties, feedback regulation offers a means to modulate enzyme function in broader pathways. In this scenario, the end product of a pathway binds upstream enzymes—often the first committed step—to slow or halt its own production. This negative feedback loop helps maintain metabolic balance.

Inhibition

An additional layer of control comes from inhibition, wherein molecules bind the enzyme to reduce or prevent its activity:

• Competitive inhibitors compete directly with the substrate for the active site, raising the effective substrate concentration needed to achieve a given reaction rate.
• Non-competitive inhibitors bind elsewhere on the enzyme, affecting activity regardless of how much substrate is present.
• Mixed inhibitors can bind either the free enzyme or the enzyme–substrate complex, exerting more nuanced effects.
• Uncompetitive inhibitors predominantly associate with the enzyme–substrate complex, shifting the reaction profile in a unique way.

Regulatory enzymes

Some regulatory enzymes have specialized structural features or undergo modifications that alter their catalytic behavior.

Allosteric enzymes contain sites separate from the active site, where binding of an effector molecule modifies the enzyme’s shape and function, either activating or inhibiting it.

Others are covalently-modified by processes such as phosphorylation, methylation, or acetylation, which can promptly switch an enzyme on or off.

A zymogen represents an inactive precursor form of an enzyme, requiring a specific biochemical alteration—like cleavage of a peptide fragment—to become active.