4.2 Catalysis and Function

Enzymes are the superheroes of cellular energetics, speeding up reactions that keep us alive. They lower activation energy, making it easier for molecules to react. Without them, our cells would be sluggish, and life as we know it wouldn't exist.

Understanding how enzymes work is key to grasping cellular energetics. Their specificity, regulation, and response to factors like temperature and pH are crucial. This knowledge helps us see how cells maintain energy balance and adapt to changing conditions.

Enzymes as Biological Catalysts

Enzymes as Catalysts

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• Enzymes are proteins that act as biological catalysts to speed up the rate of chemical reactions in living organisms without being consumed in the process
• Enzymes lower the activation energy required for a reaction to occur by providing an alternative pathway for the reaction, allowing it to proceed more quickly and efficiently
• Enzymes are highly specific, typically catalyzing only one specific reaction or a set of closely related reactions due to the unique shape and chemical properties of their active sites

Importance of Enzymes in Biological Systems

• Enzymes are essential for maintaining homeostasis and supporting critical biological processes such as metabolism (glycolysis), DNA replication (DNA polymerase), and cellular signaling (kinases)
• The catalytic activity of enzymes can be regulated through various mechanisms, including allosteric regulation (binding of effector molecules), covalent modification (phosphorylation), and changes in enzyme concentration or localization
• Without enzymes, many biological reactions would occur too slowly to sustain life, making them crucial for the proper functioning of cells and organisms (digestion, energy production)

Enzyme-Substrate Interactions

Active Site and Substrate Binding

• Enzymes interact with their substrates through the active site, a specific region of the enzyme that binds to the substrate and facilitates the chemical reaction
• The active site contains amino acid residues that form specific interactions with the substrate, such as hydrogen bonds, ionic bonds, and hydrophobic interactions, which help to orient and stabilize the substrate for the reaction
• The induced fit model suggests that the binding of the substrate to the enzyme causes a conformational change in the enzyme's active site, allowing for a tighter and more specific interaction between the enzyme and substrate

Enzyme-Substrate Complex and Catalysis

• The enzyme-substrate complex is a temporary association between the enzyme and substrate that forms just before the catalytic reaction occurs. The complex lowers the activation energy and increases the reaction rate
  • Example: In the enzyme-substrate complex of the enzyme lysozyme and its substrate, a bacterial cell wall, the active site of lysozyme binds to and strains the substrate, making it more susceptible to hydrolysis
• After the reaction is complete, the products are released from the active site, and the enzyme returns to its original conformation, ready to bind to another substrate molecule
  • Example: In the case of the enzyme lactase, which breaks down lactose into glucose and galactose, the products (glucose and galactose) are released from the active site after the hydrolysis reaction is complete

Factors Affecting Enzyme Activity

Temperature and pH

• Temperature affects enzyme activity by influencing the kinetic energy of the molecules and the stability of the enzyme's structure. Enzymes typically have an optimal temperature range where their activity is highest, and extreme temperatures can denature the enzyme and reduce its activity
  • Example: The enzyme catalase, which breaks down hydrogen peroxide, has an optimal temperature around 37°C (human body temperature). At higher temperatures, the enzyme denatures and loses its activity
• pH affects enzyme activity by altering the ionization state of the amino acid residues in the active site, which can disrupt the enzyme-substrate interactions. Each enzyme has an optimal pH range where its activity is highest
  • Example: Pepsin, a digestive enzyme found in the stomach, has an optimal pH around 2 (acidic environment of the stomach). At higher pH levels, pepsin's activity decreases significantly

Substrate and Enzyme Concentration

• Substrate concentration affects the rate of enzyme-catalyzed reactions. At low substrate concentrations, the reaction rate increases linearly with increasing substrate concentration until the enzyme becomes saturated and the rate reaches a maximum ($V_{max}$)
• Enzyme concentration also influences the reaction rate. Increasing the enzyme concentration will increase the reaction rate until the substrate becomes limiting
  • Example: In the enzyme-catalyzed reaction of sucrase breaking down sucrose, increasing the concentration of sucrose (substrate) will increase the reaction rate until all sucrase enzymes are occupied, reaching $V_{max}$. Further increasing the sucrose concentration will not increase the rate beyond this point

Inhibitors and Regulation

• Inhibitors can reduce or block enzyme activity by binding to the enzyme and interfering with its ability to bind to the substrate or catalyze the reaction. Competitive inhibitors compete with the substrate for the active site, while non-competitive inhibitors bind to other regions of the enzyme and alter its conformation
  • Example: Cyanide is a non-competitive inhibitor of the enzyme cytochrome c oxidase, which is essential for cellular respiration. Cyanide binds to the enzyme at a site other than the active site, altering its conformation and preventing it from functioning properly
• Allosteric regulation involves the binding of molecules (effectors) to sites other than the active site, causing conformational changes that affect the enzyme's activity. Allosteric effectors can be either activators or inhibitors
  • Example: The enzyme phosphofructokinase, which catalyzes a key step in glycolysis, is allosterically inhibited by high levels of ATP (end product of glycolysis) and activated by AMP (indicator of low energy levels)
• Covalent modifications, such as phosphorylation or glycosylation, can alter the activity of enzymes by changing their conformation or affecting their interactions with other molecules
  • Example: The enzyme glycogen phosphorylase, which breaks down glycogen into glucose monomers, is activated by phosphorylation in response to hormonal signals such as glucagon or adrenaline

Enzyme Kinetics: Graphical Analysis

Michaelis-Menten Kinetics

• Michaelis-Menten kinetics describes the relationship between substrate concentration and reaction rate for many enzymes. The Michaelis-Menten equation relates the reaction rate ($v$) to the maximum reaction rate ($V_{max}$) and the Michaelis constant ($K_m$)
  • $v = \frac{V_{max}[S]}{K_m + [S]}$
• The Michaelis constant ($K_m$) is the substrate concentration at which the reaction rate is half of the maximum rate ($V_{max}$). A lower $K_m$ indicates a higher affinity of the enzyme for the substrate, while a higher $K_m$ indicates a lower affinity
  • Example: The enzyme acetylcholinesterase, which breaks down the neurotransmitter acetylcholine, has a very low $K_m$, indicating a high affinity for its substrate and ensuring rapid clearance of acetylcholine from the synaptic cleft

Lineweaver-Burk Plots

• Lineweaver-Burk plots (double-reciprocal plots) are used to linearize the Michaelis-Menten equation, allowing for the determination of $V_{max}$ and $K_m$ from experimental data. The y-intercept of the Lineweaver-Burk plot represents $1/V_{max}$, while the x-intercept represents $-1/K_m$
  • $\frac{1}{v} = \frac{K_m}{V_{max}}\frac{1}{[S]} + \frac{1}{V_{max}}$

Graphical Representations of Enzyme Inhibition and Activity

• Enzyme kinetic graphs can be used to distinguish between different types of enzyme inhibition. Competitive inhibition increases the apparent $K_m$ without affecting $V_{max}$, while non-competitive inhibition decreases $V_{max}$ without changing $K_m$
  • Example: In the presence of a competitive inhibitor, the Lineweaver-Burk plot will show an increased slope (higher apparent $K_m$) but the same y-intercept ($1/V_{max}$) compared to the uninhibited reaction
• The effects of pH and temperature on enzyme activity can be visualized using graphical representations, such as bell-shaped curves showing the optimal pH or temperature range for the enzyme
• Progress curves, which plot product formation over time, can provide information about the initial reaction rate, the presence of inhibitors, and the stability of the enzyme under the given reaction conditions
  • Example: A progress curve showing a decrease in the rate of product formation over time may indicate the presence of an inhibitor or the denaturation of the enzyme due to unfavorable conditions