26.10 Enzymes and Coenzymes

Enzyme Structure and Function

Enzymes are biological catalysts that speed up chemical reactions in living organisms. Without them, most biochemical reactions would be far too slow to sustain life. Understanding how enzymes work, how they're classified, and what helper molecules they need is central to connecting protein structure (from earlier in this unit) to biological function.

Enzyme Function as Catalysts

Enzymes accelerate reactions without being consumed or permanently altered in the process. They can speed up reactions by factors of $10^3$ to $10^{17}$ compared to uncatalyzed reactions, bringing them to physiologically relevant rates.

What makes enzymes so effective is their specificity. Each enzyme catalyzes only one reaction (or a few closely related ones) because of the unique three-dimensional shape of its active site, the region where the substrate binds and the reaction occurs.

How enzymes work at an energy level:

• They lower the activation energy ($E_a$), which is the minimum energy reactants need to reach the transition state and form products.
• By lowering $E_a$, a larger fraction of reactant molecules have enough energy to react at body temperature.
• Enzymes do not change the equilibrium of a reaction. They only change how fast equilibrium is reached. The ratio of products to reactants at equilibrium stays the same.

Classification System for Enzymes

The International Union of Biochemistry and Molecular Biology (IUBMB) classifies enzymes into six categories based on the type of reaction they catalyze:

1. Oxidoreductases: catalyze oxidation-reduction reactions. Alcohol dehydrogenase, for example, oxidizes ethanol to acetaldehyde in the liver.
2. Transferases: transfer a functional group from one molecule to another. Aminotransferases move amino groups between molecules, which is key in amino acid metabolism.
3. Hydrolases: break bonds by adding water (hydrolysis). Lipases hydrolyze triglycerides into fatty acids and glycerol during fat digestion.
4. Lyases: add or remove groups from substrates without hydrolysis or oxidation. Decarboxylases, for instance, remove carboxyl groups (as $CO_2$) from amino acids.
5. Isomerases: catalyze intramolecular rearrangements (isomerizations). Glucose isomerase converts glucose to fructose by rearranging atoms within the same molecule.
6. Ligases: form new covalent bonds, coupled with the hydrolysis of ATP to provide energy. DNA ligase joins DNA fragments during replication and repair.

A helpful way to remember the order: Old Trees Have Large Interesting Leaves (Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases).

Enzyme Kinetics and Regulation

Michaelis-Menten kinetics describes how reaction rate depends on substrate concentration. At low substrate concentrations, rate increases roughly linearly as more substrate is available. At high concentrations, the enzyme becomes saturated and the rate plateaus at $V_{max}$. The $K_m$ (Michaelis constant) is the substrate concentration at which the reaction rate is half of $V_{max}$. A low $K_m$ means the enzyme has high affinity for its substrate.

Enzyme activity can be regulated in several ways:

• Competitive inhibition: an inhibitor resembles the substrate and binds directly to the active site, blocking the substrate. This can be overcome by increasing substrate concentration.
• Noncompetitive inhibition: an inhibitor binds to a site other than the active site, changing the enzyme's shape so it can't catalyze the reaction effectively. Increasing substrate concentration does not overcome this.
• Allosteric regulation: regulatory molecules bind to a site separate from the active site (an allosteric site), either activating or inhibiting the enzyme. This allows fine-tuned control of metabolic pathways.

Cofactors and Coenzymes

Many enzymes can't function with just their protein structure alone. They need non-protein helper molecules to carry out catalysis.

Cofactors vs. Coenzymes in Enzyme Function

Cofactors is the broad term for any non-protein molecule required for enzyme activity. These fall into two categories:

• Inorganic cofactors: metal ions such as $Fe^{2+}$, $Mg^{2+}$, and $Zn^{2+}$. These often help stabilize the enzyme's structure or participate directly in the catalytic mechanism (for example, $Zn^{2+}$ in carbonic anhydrase).
• Coenzymes: organic molecules that participate in the enzymatic reaction. They are often derived from vitamins, which is one reason vitamins are essential nutrients.

Key coenzymes and their roles:

• $NAD^+$ (from niacin/vitamin B3) and FAD (from riboflavin/vitamin B2): serve as electron carriers in oxidation-reduction reactions. $NAD^+$ accepts a hydride ion ($H^-$) to become $NADH$.
• Coenzyme A (from pantothenic acid/vitamin B5): carries and transfers acyl groups, playing a central role in fatty acid metabolism and the citric acid cycle.
• Thiamine pyrophosphate (from thiamine/vitamin B1): assists in decarboxylation reactions.

Unlike substrates, coenzymes are not permanently changed. They can be regenerated and recycled to participate in multiple rounds of catalysis. They also are not permanently bound to the enzyme and can dissociate after the reaction.