Metabolism and Glycolysis Notes

Microbial Metabolism

  • Definition: Metabolism encompasses the complete set of biochemical reactions occurring within cells, essential for sustaining life by managing both energy generation and cellular synthesis.

  • Catabolic Pathways:

    • Function: These pathways involve the breakdown of large, complex molecules (e.g., polysaccharides, proteins, lipids) into smaller, simpler constituents.

    • Coupled Reactions: Catabolic reactions are exergonic (energy-releasing) and are typically coupled with endergonic (energy-requiring) reactions, storing the liberated energy in carrier molecules like ATP and NADH.

    • Enzymatic Role: Enzymes serve as biological catalysts, significantly reducing the activation energy (Gibbs free energy of activation, \Delta G^\ddagger) required to reach the transition state, thereby accelerating reaction rates without altering the overall free energy change (\Delta G) of the reaction.

  • Energy Transfer: This process links specific catabolic reactions to anabolic biosynthesis and various cellular functions (e.g., active transport, motility, reproduction) by supplying readily available chemical energy.

Microbial Metabolism

  • Core Principle: All living cells necessitate a continuous supply of energy for essential activities such as movement, growth, reproduction, and the maintenance of structural integrity.

  • Types:

    • Catabolism: These are degradative processes that release chemical energy, often captured in the form of ATP, NADH, and FADH₂. These pathways are generally oxidative.

    • Anabolism: These are synthetic processes that demand energy to construct complex macromolecules from simpler precursor molecules. Energy for anabolic reactions is typically furnished by catabolic pathways.

Electron Transport and Acceptors

  • Oxygen Utilization:

    • Many microorganisms primarily use oxygen (O_2) for efficient growth.

    • Oxygen functions as the terminal electron acceptor (TEA) within the electron transport chain (ETC).

    • This specific process is designated Aerobic Respiration, characterized by a high ATP yield.

Energy Carriers and Electron Transfer

  • Key Molecules:

    • NADH, FADH₂, ATP: These are fundamental energy carriers responsible for the transfer of energy and electrons during metabolic redox reactions. NADH and FADH₂ transport high-energy electrons derived from nutrient oxidation, while ATP acts as the direct, immediately usable cellular energy currency.

  • Functions:

    • Molecules like NADH serve as electron donors in electron transport chains or certain anabolic pathways, whereas NAD⁺ acts as an electron acceptor in catabolic reactions.

  • NAD⁺ Reduction Reaction:

    • Reaction: NAD^+ + 2H^+ + 2e^- \rightarrow NADH + H^+

    • Significance: NADH sequesters considerably more potential energy (within its high-energy electrons) than a single ATP molecule and is crucial for cellular energy generation by contributing these electrons to the ETC.

Coenzyme Overview

  • Flavin Adenine Dinucleotide (FAD):

    • Reduced form: FADH₂; Oxidized form: FAD.

    • Reduction by: The addition of two electrons and two protons (2H^+}). FAD is frequently involved in reactions that form carbon-carbon double bonds, as seen in the succinate dehydrogenase reaction of the TCA cycle.

  • ATP Composition:

    • Structure: Composed of an adenine base, a ribose sugar, and three phosphate groups interconnected by high-energy phosphodiester bonds.

    • ATP Formation through: ADP + P_i \rightarrow ATP
      The terminal phosphate bond in ATP is a high-energy phosphodiester bond that releases a substantial amount of energy (approximately -\Delta G = 7.3 kcal/mol under standard conditions) upon hydrolysis.

Mechanisms of ATP Energy Transfer

ATP contains three phosphate molecules that yield energy upon hydrolysis. The three phosphates are:

  1. Hydrolysis-releasing phosphate (Pi)

  2. Hydrolysis-releasing pyrophosphate (PPi)

  3. Phosphorylation of an organic molecule

All these mechanisms underscore ATP's indispensable role as the primary energy currency, efficiently linking energy-releasing (exergonic) reactions to energy-requiring (endergonic) cellular work.

Substrate-Level Phosphorylation

  • Definition: This is a direct metabolic reaction where ATP (or GTP) is formed by transferring a phosphate group from a high-energy substrate molecule directly to ADP (or GDP). This process is independent of oxygen or an electron transport chain.

  • Enzymatic Requirement: This direct energy transfer critically depends on the activity of a kinase enzyme (e.g., phosphoglycerate kinase, pyruvate kinase in glycolysis) to catalyze the phosphate group transfer.

  • Renewability of ATP: ATP is constantly recycled within organisms; energy derived from nutrient catabolism (food intake) is used to resynthesize ATP from ADP and P_i, which in turn fuels subsequent cellular activities (anabolism).

Catabolism Overview: Microbial Nutrition

  • Microbial Substrate: The catabolic breakdown of complex polysaccharides (e.g., starch, glycogen) into constituent monosaccharides (e.g., glucose), which are then further metabolized, often via glycolysis, into pyruvate.

  • Further Catabolism:

    • Pyruvate: This central metabolite can proceed via several pathways depending on the organism and environmental conditions. It can be fermented to various end-products (e.g., lactate, ethanol) or undergo complete oxidation in the tricarboxylic acid (TCA) cycle to yield CO^2 and H2O, generating substantial ATP.

    • Lipids and Amino Acids: These complex macromolecules are also degraded. Lipids are broken down into glycerol and fatty acids; glycerol can enter glycolysis intermediates, and fatty acids are catabolized through \beta-oxidation to produce acetyl-CoA, which feeds into the TCA cycle. Amino acids undergo deamination and enter catabolic pathways at various points, commonly yielding pyruvate, acetyl-CoA, or TCA cycle intermediates.

Nutritional Types of Organisms

Organisms can be classified based on their nutritional needs and metabolic strategies:

  • Autotrophs: Organisms that produce their own food through processes like photosynthesis or chemosynthesis.

  • Heterotrophs: Organisms that rely on consuming organic substances for energy and nutrients, including animals and many fungi.

  • Phototrophs: Organisms that obtain energy from light; this includes plants and certain bacteria.

  • Chemotrophs: Organisms that obtain energy from chemical compounds, often through the oxidation of inorganic substances.

Classification Based on Energy Source:

  • Phototrophs: Organisms that harness light energy (solar radiation) and convert it into chemical energy (ATP and NADPH) via photosynthesis. Examples include plants, algae, and cyanobacteria.

  • Chemotrophs: Organisms that secure energy from the oxidation of chemical compounds (either inorganic or organic). This energy is liberated from redox reactions and subsequently conserved in ATP.

  • Based on Electron Source:

    • Lithotrophs: (Literally "rock-eaters") These organisms employ reduced inorganic substances as electron donors. Many lithotrophs are chemosynthetic.

    • Organotrophs: These organisms obtain electrons from organic compounds (e.g., glucose, acetate, succinate). This category includes most heterotrophic bacteria, fungi, and all animals.

Chemoorganotrophic Fueling Processes

  • Definition: Also recognized as chemoheterotrophs, these organisms acquire both their energy and electrons from organic compounds and utilize organic carbon sources for their biosynthesis.

  • Catabolic Energy Processes:

    • Aerobic Respiration: A highly efficient catabolic process where internal organic electron donors are oxidized, and electrons are relayed through an electron transport chain to oxygen (O_2), which serves as the final electron acceptor. This pathway generates a large quantity of ATP predominantly through oxidative phosphorylation.

    • Anaerobic Respiration: Similar to aerobic respiration in its use of an electron transport chain and oxidative phosphorylation, but it involves alternative oxidized inorganic molecules e.g. Nitrate (NO3^{-} ), Sulfate(SO4^{2-} , Carbonate(CO3^{2-}), and Fumerate(Fe^{3+}) as terminal electron acceptors instead of oxygen. This typically results in a lower ATP yield than aerobic respiration.

    • Fermentation: A less efficient catabolic process that proceeds in the absence of an external terminal electron acceptor. It completes catabolism without involving an electron transport chain. ATP production relies exclusively on substrate-level phosphorylation, and electrons are transferred from the initial substrate to an endogenous organic electron acceptor (often an intermediate like pyruvate or its derivatives).

Electron Transport Chain Involvement

  • Aerobic Processes: In aerobic respiration, a sequence of membrane-bound electron carrier molecules (e.g., flavoproteins, cytochromes, quinones) facilitates the passage of electrons from reduced carriers (NADH, FADH₂) to oxygen which is subsequently reduced to water. This crucial process occurs in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes.

  • Anaerobic Processes: Anaerobic respiration follows the same fundamental principle, but the final electron acceptor is an inorganic molecule other than oxygen (e.g., NO3^{-},SO4^{2-},CO2,Fe^{3+},SeO4^{2-} ). The specific components of the ETC can vary based on the particular electron acceptor used.

  • Proton Motive Force (PMF): During electron transport, the energy released from redox reactions is harnessed to actively pump protons (H+) across the cellular membrane, establishing an electrochemical proton gradient (PMF). This PMF represents stored potential energy, which is then utilized by ATP synthase to drive the synthesis of ATP from ADP and Pi (oxidative phosphoralation).

Fermentation Process

  • Mechanism: Fermentation employs an endogenous electron acceptor, typically an organic molecule generated as an intermediate within the same organic energy pathway (e.g., pyruvate or an aldehyde derived from pyruvate). The primary goal of fermentation is to regenerate oxidized NAD⁺ (from NADH), thereby allowing glycolysis to continue producing ATP via substrate-level phosphorylation when an external electron acceptor for an ETC is unavailable.

  • Importance: This process does not involve the electron transport chain, oxygen, or any other external electron acceptors. Consequently, ATP is synthesized solely through substrate-level phosphorylation, yielding significantly less ATP compared to respiration. Despite the lower yield, fermentation enables cells to generate ATP quickly under anaerobic conditions and is vital for regenerating NAD⁺ to sustain glycolysis.

Major Nutritional Types Recapped

  • Nutritional types represent various combinations of energy source, electron source, and carbon source:

    • Photolithoautotrophs: Obtain energy from light, use inorganic compounds (litho) as electron donors, and fix CO_2 (auto) as their exclusive carbon source. Examples include cyanobacteria, purple, and green sulfur bacteria.

    • Chemolithoautotrophs: Acquire energy from the oxidation of inorganic chemicals (chemo), utilize inorganic compounds (litho) as electron donors, and fix CO_2 (auto) for their carbon requirements. Examples include nitrifying bacteria and sulfur-oxidizing bacteria.

    • Chemoorganoheterotrophs: Derive both energy and electrons from organic carbon sources (organo), and also use organic compounds as their carbon source (hetero). This group is prevalent among pathogens and encompasses most non-photosynthetic bacteria, all fungi, protozoa, and animals.

    • Photoorganoheterotrophs: Organisms that utilize light energy (photo) and serve organic compounds as both their electron donors and carbon sources (organo-hetero). Examples include certain types of purple non-sulfur bacteria, and green non-sulfer bacteria.

    • Chemolithoheterotrophs:Organisms that obtain energy by oxidizing inorganic compounds (chemo), and utilize organic compounds as their carbon source (hetero). Examples include sulfur-oxidizing bacteria, hydrogen-oxidizing bacteria, methanogens, nitrifying bacteria, and iron-oxidizing bacteria.

Reactions Summary

  • Despite the immense diversity in energy and carbon acquisition among organisms, all living cells share fundamental metabolic requirements that must be met by their fueling reactions:

    • ATP: As the essential, readily available energy currency that powers nearly all intracellular activities, from biosynthesis to active transport.

    • Reducing Power: Crucial electrons, carried by molecules such as NADH, NADPH, and FADH₂, are necessary for reductive biosynthesis (anabolism) and to drive electron transport chains for ATP generation (catabolism).

    • Precursor Metabolites: Essential intermediate molecules that serve as foundational building blocks for the synthesis of complex macromolecules, including amino acids, nucleotides, lipids, and carbohydrates.

Pathways for Glucose to Pyruvate

  • Microorganisms utilize three primary routes for the catabolism of glucose to pyruvate, each characterized by distinct inputs, intermediate compounds, and outputs:

    1. Embden-Meyerhof Pathway (Glycolysis): The most ubiquitous pathway, found universally in plants, animals, and numerous microorganisms.

    2. Entner-Doudoroff Pathway: An alternative pathway, predominantly observed in certain Gram-negative bacteria.

    3. Pentose Phosphate Pathway: An amphibolic pathway that can operate concurrently with the other two, performing vital roles in biosynthesis and protection against oxidative stress.

Glycolysis Pathway Details

  • Location: This fundamental metabolic pathway takes place within the cytoplasmic matrix of virtually all microorganisms, plants, and animal cells.

  • Oxygen Conditions: Glycolysis is an anaerobic process, meaning it functions effectively both in the presence and absence of molecular oxygen. It’s products can subsequently enter either through aerobic respiration (oxygen is present) or fermentation (no oxygen present).

  • Stages: Glycolysis is systematically divided into two principal phases:

    • Energy Investment Phase: (Reactions 1-5)

    • Glucose undergoes two phosphorylation events, consuming 2 ATP molecules to activate it. The first ATP creates glucose-6-phosphate, and the second ATP generates fructose-1,6-bisphosphate.

    • Fructose-1,6-bisphosphate is then enzymatically cleaved by aldolase into two three-carbon molecules: dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P).

    • DHAP is rapidly isomerized to G3P by triose phosphate isomerase, ensuring both three-carbon molecules can proceed into the subsequent phase.

    • Energy Yield Phase: (Reactions 6-10)

    • Each G3P molecule is oxidized, and an inorganic phosphate group is added, yielding 1,3-bisphosphoglycerate and reducing NAD⁺ to NADH. Since two G3P molecules are processed per glucose, 2 NADH molecules are generated.

    • Substrate-level phosphorylation occurs twice in this phase for each G3P molecule, collectively producing 4 ATP molecules (two from 1,3-bisphosphoglycerate to 3-phosphoglycerate, and an additional two from phosphoenolpyruvate to pyruvate).

    • The ultimate product of this phase, from the initial glucose molecule, is 2 molecules of pyruvate.

Summary of Glycolysis Outcomes

  • Main Product: The catabolism of each glucose molecule yields 2 molecules of pyruvate.

  • Energy Output: Glycolysis results in a net gain of 2 ATP molecules (4 gross ATP produced minus 2 ATP consumed in the investment phase) and 2 NADH molecules.

Overview of Glycolysis:

1 Glucose inputs 2 ATP to form 2 Glyceraldehyde-3-phosphate to then yield 4 ATP and 2 NADH to produce 2 pyruvates.

Entner-Doudoroff Pathway Attributes

  • Utilization: This pathway is employed by specific Gram-negative bacteria (e.g., Pseudomonas, Azotobacter, Rhizobium, Agrobacterium) and a few Gram-positive bacteria (e.g., Enterococcus faecalis) as an alternative or supplementary route for glucose catabolism alongside glycolysis.

  • Key Steps: It features unique enzymes such as KDPG aldolase and 6-phosphogluconate dehydratase. Glucose is initially converted to 6-phosphogluconate, which is then transformed into 2-keto-3-deoxy-6-phosphogluconate (KDPG), finally cleaved into pyruvate and glyceraldehyde-3-phosphate.

  • Yield: Per glucose molecule, the Entner-Doudoroff pathway generates 1 ATP (via substrate-level phosphorylation), 1 NADPH (utilized for biosynthesis or convertible to NADH), and 1 NADH directly.

Pentose Phosphate Pathway Description

  • Also Known As: This pathway is also referred to as the Hexose Monophosphate Pathway (HMP) or the phosphogluconate pathway.

  • Functionality: It is a highly versatile pathway capable of operating concurrently with glycolysis and/or the Entner-Doudoroff pathway within the cell, providing metabolic flexibility.

  • Category: The pentose phosphate pathway is classified as an amphibolic pathway because it fulfills critical roles in both anabolic (biosynthesis) and catabolic (degradation) processes.

  • Key Contributions:

    • NADPH Production: Its primary function is the generation of NADPH, which is indispensable for reductive biosynthesis (e.g., fatty acid and steroid synthesis) and for safeguarding cells against oxidative stress (e.g., by reducing glutathione).

    • Precursor Metabolites: It produces various essential intermediate molecules, notably erythrose-4-phosphate (a precursor for aromatic amino acids) and ribose-5-phosphate (a precursor for nucleotides, DNA, and RNA synthesis).

    • Interconversion of Sugars: This pathway enables the interconversion of different sugar types, including hexoses (6-carbon sugars), pentoses (5-carbon sugars), and tetroses (4-carbon sugars).