Microbial Metabolism
BASICS OF MICROBIAL METABOLISM
METABOLISM
Definition: Metabolism refers to the total chemical processes within a living organism.
Categories of Metabolism
Catabolism:
Describes the processes that degrade macromolecules into smaller molecules.
Yield energy, primarily in the form of ATP, and release heat.
Anabolism:
Refers to the processes involved in the synthesis of larger molecules from smaller precursor molecules.
Utilizes available energy (typically in the form of ATP).
Amphibolic pathways:
Pathways that involve both anabolic and catabolic reactions.
ACCOMPLISHMENTS OF METABOLISM
Metabolism can fulfill several functions:
Assembles smaller molecules into large macromolecules for the cell, utilizing ATP to form bonds (anabolism).
Breaks down macromolecules into smaller molecules, a process that yields energy (catabolism).
Collects energy and expends it primarily in the form of ATP or as heat.
SIMPLIFIED MODEL OF METABOLISM
Relative Complexity of Molecules:
Glucose and other macromolecules can enter into catabolic pathways (e.g., glycolysis) and anabolic pathways (e.g., building blocks like amino acids).
Products of metabolism can include varying macromolecules such as proteins, nucleotides, and lipids.
Processes:
Nutrients enter the cell from external sources or are sourced from internal precursor molecules.
Enzymatic pathways involved in both catabolism and anabolism include Glycolysis, the Krebs cycle, and the respiratory chain.
Some assembly reactions may occur spontaneously but do utilize energy in anabolic processes.
ENZYMES: CATALYZING THE CHEMICAL REACTIONS OF LIFE
Definition: Catalysts are substances that speed up the rate of chemical reactions without undergoing any permanent changes themselves.
Mechanism of Enzymatic Action
Enzymes help in overcoming activation energy barriers, allowing reactions to proceed by:
Increasing thermal energy (heating) to boost molecular velocity.
Increasing the concentration of reactants to elevate the rate of collisions between molecules.
Functioning as biological catalysts (enzymes) to facilitate these processes.
CHECKLIST OF ENZYME CHARACTERISTICS 1
Composed most often of proteins, with some requiring cofactors.
Act as organic catalysts, significantly speeding up cellular reactions.
Reduce the activation energy needed for a chemical reaction to occur.
Exhibit unique characteristics including shape, specificity, and function.
Enable metabolic reactions to take place at a biologically viable pace.
CHECKLIST OF ENZYME CHARACTERISTICS 2
Have an active site for substrate binding.
Are much larger than their substrates.
Associate closely with substrates but do not integrate into the final products of the reaction.
Are not consumed or permanently altered by the reaction.
Can be recycled, performing repeatedly even at low concentrations.
Are affected by environmental conditions such as temperature and pH.
Can be regulated by feedback and genetic control mechanisms.
HOW DO ENZYMES WORK?
Substrates: Reactant molecules that enzymes act upon.
Enzymes bind with substrates and facilitate the transformation of the substrate:
They do not become part of the products.
They are not consumed or modified permanently by the reaction.
Capable of functioning repeatedly.
ENZYMES CATEGORIZATION
Simple enzymes: Comprise only protein molecules.
Conjugated enzymes: Consist of a protein component (apoenzyme) and non-protein components (cofactors).
Coenzyme: An organic compound that works with an enzyme.
Holoenzyme: The complete enzyme with its bound cofactors.
Ribozymes: RNA molecules demonstrating enzymatic activity.
ENZYMATIC ACTIVITY
Various types of enzymes are classified based on their functions:
Oxidoreductases and dehydrogenases: Responsible for transferring electrons and hydrogen.
Transferases: Enzymes that transfer functional groups.
Hydrolases: Enzyme class that cleaves covalent bonds using water.
Lyases: Enzymes that can form or break double bonds.
Isomerases: Change substrates into their isomeric forms.
Ligases: Form bonds using ATP while releasing water.
SAMPLING OF ENZYMES, THEIR SUBSTRATES, AND THEIR REACTIONS
Lactase (β-D-galactosidase):
Class: Hydrolase
Substrate: Lactose
Action: Breaks lactose into glucose and galactose.
Penicillinase (β-lactamase):
Class: Hydrolase
Substrate: Penicillin
Action: Hydrolyzes the beta-lactam ring.
DNA polymerase (DNA nucleotidyl-transferase):
Class: Transferase
Substrate: DNA nucleosides
Action: Synthesizes a DNA strand, using a complementary strand as a template.
Lactate dehydrogenase:
Class: Oxidoreductase
Substrate: Pyruvic acid
Action: Converts pyruvic acid to lactic acid.
Oxidase (Cytochrome oxidase):
Class: Oxidoreductase
Substrate: Molecular oxygen (O2)
Action: Catalyzes reduction of O2 through the addition of electrons and hydrogen.
ENZYME-SUBSTRATE REACTIONS
Enzyme-substrate reactions can occur rapidly, often reaching up to millions of times per second.
Types of Enzymes by Functionality
Location-based classification:
Endoenzymes: Function within cellular confines.
Exoenzymes: Function outside the cell.
Presence-based classification during life cycle:
Constitutive enzymes: Constantly present in relatively stable amounts.
Regulated enzymes: Their abundance fluctuates, controlled in their production.
ENERGY IN CELLS
Exergonic reactions: Release energy and provide energy that is available for cellular work.
Endergonic reactions: Require energy input to proceed.
Coupling of reactions: Exergonic and endergonic reactions often occur together to balance energy flow.
ENERGY AND METABOLISM
Metabolic pathways involving oxidoreductases and dehydrogenases depict electron transport mechanisms that release energy, which is harnessed in ATP synthesis.
Key coenzymes acting as electron carriers include nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD).
Phosphorylation: The process of adding a phosphate group to adenosine diphosphate (ADP) or another molecule to store energy.
In anabolic processes, ATP undergoes hydrolysis to ADP and a phosphate group, unleashing previously captured energy for biosynthesis.
ADENOSINE TRIPHOSPHATE (ATP)
Definition: ATP is the primary energy carrier in cells.
When utilized in a reaction, it needs to be regenerated.
ATP replenishment and utilization form a continuous cycle.
Substrate-level phosphorylation: Refers to the direct generation of ATP from a phosphorylated compound transferring its phosphate to ADP directly.
OVERVIEW OF CATABOLISM
Three primary catabolic processes:
Aerobic respiration
Anaerobic respiration
Fermentation
Glycolysis: The most common pathway for glucose degradation.
OVERVIEW OF THE THREE MAIN PATHWAYS OF CATABOLISM
AEROBIC RESPIRATION:
Utilizes oxygen as the final electron acceptor.
Produces approximately 36 ATP molecules per glucose.
ANAEROBIC RESPIRATION:
Employs oxidized compounds like nitrates as final electron acceptors.
Generally produces fewer ATP molecules compared to aerobic respiration.
FERMENTATION:
Utilizes organic compounds as electron acceptors.
Outputs only 2 ATP molecules per glucose.
GLUCOSE – THE MOST COMMON NUTRIENT
Glucose can enter three metabolic pathways:
Aerobic respiration: With oxygen, yielding approximately 36 ATPs per glucose.
Anaerobic respiration: Using oxidized compounds; similar to aerobic but yields fewer ATPs.
Fermentation: Employs organic compounds with only 2 ATPs produced from glucose.
AEROBIC RESPIRATION IN EUKARYOTES
Glycolysis: A catabolic process breaking glucose down into two pyruvic acid molecules while generating ATP and NADH.
Krebs Cycle: An amphibolic pathway producing ATP and reduced coenzymes (FADH2 and NADH).
Electron Transport Chain: Transports electrons from reduced coenzymes through mitochondrial membranes to build a proton gradient used by ATP synthase for ATP production.
THEORETIC ATP YIELD FROM AEROBIC RESPIRATION
Basic Outputs:
Glycolysis yields 2 ATPs, further breakdown related to Krebs Cycle and Electron Transport can yield up to a total of 36-38 ATPs per glucose molecule.
Summary of Theoretical Yields
The maximum yield of ATP can equal 40, subtracting for initial ATP usage in glycolysis leads to a net maximum of 38 ATP.
Actual yields may vary in eukaryotic cells due to energy consumption relating to NADH transport across mitochondrial membranes.
OTHER PRODUCTS OF RESPIRATION
Byproducts generated include six CO2 from Krebs cycle, six O2 consumed during electron transport, and a total net of six H2O produced with two from glycolysis and two from the Krebs cycle.
AEROBIC RESPIRATION IN PROKARYOTES
Similar to eukaryotic respiration with notable differences:
Glycolysis may occur inside or outside of the cell.
The Krebs Cycle operates within the cytoplasm.
The proton gradient during electron transport is created either between the cell and outer membrane (for Gram-negative bacteria) or between the cell membrane and cell wall (for Gram-positive bacteria).
FERMENTATION
Fermentation occurs under anaerobic conditions where glucose oxidation is incomplete.
Alcoholic fermentation: Converts pyruvic acid into ethanol, primarily carried out by yeasts and certain bacteria.
Acidic fermentation: Converts pyruvic acid into various acids (lactic acid is common).
Less efficient than respiration, yielding only 2 ATPs for each glucose.
PRODUCTS OF ALCOHOLIC FERMENTATION
In organisms that convert pyruvic acid to ethanol, the process includes:
Decarboxylation of pyruvic acid to acetaldehyde.
Reduction of acetaldehyde to ethanol.
Oxidation of NADH back to NAD, allowing glycolysis to perpetuate.
PRODUCTS OF ACIDIC FERMENTATION
Pathways vary widely:
Homolactic fermentation: Lactic acid bacteria primarily convert pyruvate to lactic acid.
Heterolactic fermentation: Glucose fermentation yields a mixture of lactic acid, acetic acid, and carbon dioxide.
PRODUCTS OF MIXED ACID FERMENTATION
Family Enterobacteriaceae contain enzymatic systems to convert pyruvic acid into several acids concurrently, like acetic, lactic, succinic, and formic acids along with CO2, contributing to intestinal gas production.