Biochemistry: Enzymes, Induced Fit, Citric Acid Cycle & Electron Transport Chain

Induced Fit

• Enzymes are highly specific for the chemical reactions they catalyze among thousands of possible reactions in the human body.
• The active site of an enzyme has a shape that fits a portion of the substrate molecule, similar to how the correct key fits a door lock.
• As an enzyme attaches to the substrate, it changes its shape slightly to enable a physical embrace between the molecules, a phenomenon called induced fit.
• The substrate (for example a disaccharide) and its products (two monosaccharides) are shown in red in the descriptive diagram.
• Induced fit puts the substrate under physical or chemical stress, making it easier to break covalent bonds and initiate the chemical reaction.
• Once a covalent bond is broken, the enzyme can bind another substrate molecule to begin the process again.

Enzymes

• The sum of all chemical reactions in an organism is its metabolism.
• Enzymes are specialized proteins that lower activation thresholds and speed up many types of chemical reactions.
• Covalent bonds in molecules must be broken to initiate a chemical reaction.
• Example: hydrolysis of a disaccharide to two monosaccharides, such as sucrose being split into glucose and fructose.
• Sucrose is a glucose molecule covalently bonded to a fructose molecule derived from sugar cane and sugar beets.
• Energy, usually in the form of heat, is required for a chemical reaction to occur; the threshold amount of heat is called its activation energy.
• Adding substantial heat is often not possible or desirable with living cells because it could damage or destroy them.
• Enzymes enable metabolism to occur at lower temperatures by reducing the amount of activation energy required to break molecular bonds.
• Enzymes are catalysts that lower the barriers for chemical reactions to occur.
• Catalyst: a chemical substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change.

Activation Energy and Catalysis

• Activation energy (denoted as E_a) is the threshold energy needed for a reaction to proceed.
• Enzymes lower the activation energy, allowing reactions to occur at lower, physiologically compatible temperatures.
• Since heat alone is not a viable tool for regulating metabolism in living cells, enzymes are essential to efficient biochemistry.
• The concept of catalysis explains how enzymes speed up reactions without being consumed.

The Citric Acid Cycle (Biochemistry)

• The figure lists a path starting with Pyruvate and CoA to form Acetyl-CoA and proceed through a series of intermediates to regenerate Oxaloacetate.
• Pyruvate dehydrogenase step:
  • $\text{Pyruvate} + \text{CoA} + \text{NAD}^+ \rightarrow \text{Acetyl-CoA} + \text{CO}_2 + \text{NADH} + \text{H}^+$
• Acetyl-CoA combines with Oxaloacetate to form Citrate via Citrate Synthase.
  • $\text{Acetyl-CoA} + \text{Oxaloacetate} \rightarrow \text{Citrate}$
• Citrate is isomerized to Isocitrate via Aconitase.
• Isocitrate dehydrogenase step:
  • $\text{Isocitrate} + \text{NAD}^+ \rightarrow \text{α-Ketoglutarate} + \text{CO}_2 + \text{NADH} + \text{H}^+$
• α-Ketoglutarate dehydrogenase step: formation of Succinyl-CoA with release of CO₂ and NADH.
  • $\text{α-Ketoglutarate} + \text{NAD}^+ + \text{CoA} \rightarrow \text{Succinyl-CoA} + \text{CO}_2 + \text{NADH} + \text{H}^+$
• Succinyl-CoA synthetase step: conversion to Succinate with generation of GTP (or ATP) and release of CoA-SH.
  • $\text{Succinyl-CoA} + \text{GDP} + \text{P}_\text{i} \rightarrow \text{Succinate} + \text{CoA-SH} + \text{GTP}$
• Succinate dehydrogenase step: Succinyl-CoA to Succinate with formation of FADH₂.
  • $\text{Succinate} + \text{FAD} \rightarrow \text{Fumarate} + \text{FADH}_2$
• Fumarase step: hydration of fumarate to Malate.
  • $\text{Fumarate} + \text{H}_2\text{O} \rightarrow \text{Malate}$
• Malate dehydrogenase step: Malate to Oxaloacetate with production of NADH.
  • $\text{Malate} + \text{NAD}^+ \rightarrow \text{Oxaloacetate} + \text{NADH} + \text{H}^+$
• Overall, the cycle regenerates Oxaloacetate to continue the process.
• Legend:
  • CoA: Coenzyme A
  • Ordinary bond vs High-energy bond
  • Adenosine groups: ATP (adenosine triphosphate) and GTP (guanosine triphosphate)
  • NADH, NAD⁺, FADH₂, FAD, and related dehydrogenases
• Note: The sequence highlights key enzymes and energy carriers (NADH, FADH₂) produced during the cycle.

Electron Transport Chain

• The molecules of the electron transport chain are found in the inner membrane of the mitochondria.
• Hydrogen ions (H⁺) move down their concentration gradient toward oxygen as electrons are transferred along the chain.
• The process is aerobic and requires a constant supply of oxygen.
• The electron transport chain uses electrons from NADH and FADH₂ to pump hydrogen ions against their concentration gradient across the mitochondrial membrane.
• Final electron acceptor is oxygen, forming water.
• This flow of electrons and the resulting proton gradient drive ATP synthesis via ATP synthase.
• Overall role: convert energy stored in NADH and FADH₂ into a proton motive force and ultimately ATP.

Versatility of Cellular Respiration

• So far, glucose has been the primary focus as a fuel source for cellular respiration.
• Cellular respiration also uses other carbohydrates, fats, proteins, and nucleic acids as fuels.
• The digestive process hydrolyzes (breaks down) large food molecules into monomers that can be absorbed by the small intestine for glycolysis and the citric acid cycle.

Carbon Monoxide and Cyanide Poisoning

• Danger and poison: CO and cyanide block the transfer of electrons to oxygen in the electron transport chain.
• When electron transfer to oxygen is blocked, mitochondria cannot harvest energy from food to convert ADP to ATP.
• As a result, cells stop functioning and the organism can die, often very rapidly.
• Practical implication: exposure to CO or cyanide is an acute, life-threatening situation due to shutdown of aerobic respiration.