Enzyme Biology and Regulation

Enzymes and Catalysis

• Enzymes lower the activation energy of both

  Enzymes and Catalysis

  • Enzymes lower the activation energy of both Exergonic reactions release energy spontaneously.which require energy and do not occur spontaneously.
  • The active site of an enzyme is where a substrate binds, and it can change shape when a substrate enters - induced fit.

  Active Site

  • Typically, there is a close shape match between the active site and substrate (lock and key) - specificity, ensuring that the enzyme only catalyzes a specific reaction.
  • The active site is a three-dimensional region with a unique shape and chemical properties that allows it to bind to a specific substrate, positioning it for a chemical reaction to occur.

  reactions.

• The active site of an enzyme is where a substrate binds, and it can change shape when a substrate enters - induced fit.

Active Site

• Typically, there is a close shape match between the active site and substrate (lock and key) - specificity.
• The active site is a cleft or crevice where catalysis takes place.
• The shape of the active site can change as the substrate enters - induced fit, forming the enzyme-substrate complex.

Enzyme Catalysis Strategies

• Enzymes may form covalent bonds with the substrate itself.
• General strategies of enzyme catalysis include various ways to lower the activation energy.

Temperature and pH Effects

• Temperature and pH affect reaction rates; temperatures below or above the optimum canreduce enzyme activity by altering the enzyme's conformation, obstructing active site access, or disrupting essential electrostatic interactions, which are crucial for maintaining the enzyme's active site geometry and facilitating substrate binding. These interactions can be disrupted by pH changes, leading to a decrease in enzyme activity. Optimal pH ranges for enzyme activity can vary greatly, with some enzymes being active in acidic conditions (e.g., pepsin in the stomach) and others in alkaline conditions (e.g., trypsin in the small intestine). Temperature and pH effects are often enzyme-specific, making it essential to understand the optimal conditions for a particular enzyme to function efficiently.
• pH changes can affectpH changes affect enzyme activity by altering amino acid residues' protonation states, influencing charges, conformation, and substrate binding. pH-dependent protonation states can enhance or hinder enzyme-substrate interactions, modulating activity and thermo-stability.

Cofactors

• Cofactors are non-protein molecules that bind to enzymes, enabling them to perform their biological functions. These molecules can be either inorganic (e.g., metal ions like zinc, iron, or copper) or organic (e.g., flavin or heme groups). Cofactors can modulate enzyme activity by influencing the active site's shape, participating in catalysis, or facilitating the transfer of electrons. In some cases, cofactors are tightly bound to the enzyme, while in others, they are loosely associated or even diffuse into the enzyme's active site during catalysis. Examples of enzymes requiring cofactors include carbonic anhydrase (which uses zinc) and lactate dehydrogenase (which uses NAD+). The presence or absence of cofactors can significantly impact enzyme activity, underscoring their critical role in maintaining proper enzyme function.are required for catalysis in some enzymes, including inorganic ions (e.g., Fe, Zn, Cu) and complex organic molecules (coenzymes, e.g., vitamins, NAD+, FAD).

Enzyme Inhibition

• Inhibitors can be drugs, toxins, or normal metabolites that regulate activity.
• Types of inhibitors include:
  • Irreversible inhibitors (bind covalently, e.g., penicillin)
  • Reversible inhibitors:
    • Competitive inhibitors (bind to active site)
    • Non-competitive inhibitors (bind away from active site)

Enzyme Control

• Control mechanisms include:
  • Allosteric control (fast, <1 sec): molecule binds away from active site, stabilizing active or inactive forms
  • Covalent control (relatively fast, <1 sec): phosphorylation and dephosphorylation of enzymes
  • Genetic control (slower, seconds-minutes): regulation of enzyme expression

Feedback Inhibition

• Feedback inhibition occurs when the end product of a metabolic pathway inhibits an enzyme that catalyzes an earlier reaction in the pathway.

Examples of Enzyme Control

• In frogs, glycogen phosphorylase is regulated by both allosteric and covalent control mechanisms, involving phosphorylation and dephosphorylation.
• Wood frogs release glucose from glycogen as they freeze in winter, and this regulation is essential for their survival.

Cytochrome c in Evolutionary Studies

• Cytochrome c is used in evolutionary studies to construct clades, as its amino acid sequence varies slightly between species, allowing researchers to reconstruct phylogenetic relationships and infer evolutionary histories.
• It is a highly conserved protein, with humans and chimps having identical cytochrome c, and rhesus monkeys differing by only one amino acid

Electron Transport Chain

• Electrons lose energy as they move towards electronegative O2
• Electrons pass through various cofactors and coenzymes, resulting in the reduction of O2 to water
• About 90% of oxygen breathed in is used in this process

Electron Transport Chain Complexes

• The electron transport chain consists of 4 large protein complexes in the inner mitochondrial membrane
• Complexes 1, 2, 3, and 4 are involved in the process
• Q (ubiquinol/ubiquinone/coenzyme Q) and cytochrome c are two electron carriers involved in the process

Cytochrome c

• Cytochrome c is a small, well-conserved protein throughout evolution
• It is 100-104 amino acids long and contains a heme with a central Fe atom as a cofactor
• Cytochromes are redox-active proteins involved in electron transport and redox catalysis

Electron Transport Chain and Oxidative Phosphorylation

• The electron transport chain generates a proton gradient, which is a form of potential energy
• The gradient is used to drive the production of ATP through the process of chemiosmosis
• ATP synthase forms a pathway for protons to move down their electrochemical gradient, generating ATP

Uncouplers

• Uncouplers are proteins that move protons back across the membrane, bypassing ATP synthase
• This process converts potential energy to kinetic energy (heat), and is used in certain cells to generate heat

ATP Yield and Fermentation

• The complete breakdown of glucose produces approximately 32 ATPs
• In the absence of oxygenIn contrast to the efficient process of cellular respiration, which generates approximately 36-38 ATP molecules from one glucose molecule, fermentation (anaerobic respiration), occurring in the absence of oxygen, yields only 2 ATP molecules per glucose molecule. This process takes place in the cytosol and is characteristic of muscle cells when they are subjected to intense, short-duration exercises. During fermentation, glucose is converted into lactic acid, producing a net gain of 2 ATP molecules through substrate-level phosphorylation. Notably, this process does not involve the electron transport chain or oxidative phosphorylation, unlike cellular respiration. occurs
• Other catabolic pathways are also available for energy production

Getting Energy from Fats

• Fats are a major source of energy storage in humans and other mammals
• β-oxidation occurs in the mitochondrial matrix, producing 3 NADH, 1 FADH2, and 1 ATP per acyl unit
• The energy yield from fats is much higher than from carbohydrates