8.1 Energy, Matter, and Enzymes
3 min read•june 18, 2024
Microbes rely on to survive and thrive. They break down complex molecules for energy and build new ones for growth. Some make their own food, while others need organic compounds. reactions power these processes, moving electrons around.
Energy carriers like ATP fuel cellular activities. Enzymes speed up reactions, with their structure determining function. Inhibitors can slow enzymes down. Understanding how microbes generate and use energy is key to grasping their incredible diversity and adaptability.
Metabolism and Energy Acquisition
Role of metabolism in microbes
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- Sum of all chemical reactions within a living organism
- breaks down complex molecules releasing energy (glucose breakdown)
- uses energy to synthesize complex molecules from simpler ones (protein synthesis)
- Microbial cells rely on to generate ATP energy, synthesize essential biomolecules (proteins, nucleic acids, lipids, carbohydrates), and maintain cellular homeostasis
Autotrophs vs heterotrophs
- produce their own organic compounds using inorganic sources
- use light energy to synthesize organic compounds (cyanobacteria, purple sulfur bacteria)
- use chemical energy from inorganic compounds to synthesize organic compounds (sulfur-oxidizing bacteria, nitrifying bacteria)
- rely on organic compounds as their energy and carbon source
- obtain energy from chemical reactions involving organic compounds (most bacteria, fungi)
Oxidation-reduction in microbial metabolism
- (redox) reactions transfer electrons between molecules
- Oxidation loses electrons
- Reduction gains electrons
- Redox reactions crucial in microbial metabolism for generating energy through , driving metabolic pathways (, ), and maintaining cellular redox balance
Cellular Energy Processes and Enzymes
Energy carriers in cellular processes
- universal energy currency in living cells stores and transfers energy for cellular processes (, transport, motility)
- () involved in redox reactions accepts electrons during oxidation reactions (reduced to ) donates electrons to electron transport chain for ATP synthesis
- () coenzyme involved in redox reactions accepts electrons during oxidation reactions (reduced to NADH) donates electrons to electron transport chain for ATP synthesis
- (Nicotinamide adenine dinucleotide phosphate) coenzyme involved in anabolic reactions accepts electrons during oxidation reactions (reduced to ) provides reducing power for biosynthetic reactions
Enzyme structure in microbes
- Enzymes are proteins that catalyze chemical reactions in living cells
- Structure composed of one or more polypeptide chains with specific three-dimensional shape determined by amino acid sequence
- Key components include:
- region where binds and occurs
- non-protein molecules required for function (metal ions, vitamins)
- organic molecules that assist in enzyme catalysis (FAD, NAD+, NADP+)
Types of enzyme inhibitors
- Enzyme inhibitors are molecules that decrease or stop enzyme activity
- structurally similar to substrate bind to preventing substrate binding causing reversible inhibition that can be overcome by increasing substrate concentration affecting () but not (maximum velocity)
- bind to other than active site causing conformational changes that decrease enzyme activity with reversible or irreversible inhibition that cannot be overcome by increasing substrate concentration affecting but not
- Enzyme inhibition in microbial metabolism can disrupt essential metabolic pathways, impair energy production and cellular growth, and be exploited for development of antimicrobial agents (antibiotics, antifungals)
Thermodynamics and Bioenergetics in Microbial Metabolism
- governs energy transformations in microbial cells
- refers to the total heat content of a system, important in understanding energy changes during chemical reactions
- measures the degree of disorder in a system, increasing in spontaneous processes
- applies thermodynamic principles to biological systems
- is the minimum energy required for a reaction to occur, which enzymes lower through catalysis
- studies the rate of enzyme-catalyzed reactions, crucial for understanding metabolic regulation
Key Terms to Review (85)
$K_m$: $K_m$ is a kinetic parameter that represents the substrate concentration at which an enzyme-catalyzed reaction proceeds at half its maximum rate. It is a measure of the affinity between an enzyme and its substrate, providing insight into the efficiency of the catalytic process.
$V_{max}$: $V_{max}$ is the maximum rate at which an enzyme-catalyzed reaction can occur. It represents the maximum velocity or speed at which a particular enzyme can convert substrates into products, and it is an important parameter in understanding enzyme kinetics and the efficiency of enzymatic processes.
Activation energy: Activation energy is the minimum amount of energy required to start a chemical reaction. In biological systems, enzymes lower the activation energy needed for metabolic reactions.
Activation Energy: Activation energy is the minimum amount of energy required to initiate a chemical reaction. It is the energy barrier that must be overcome for the reaction to occur and proceed forward. Activation energy is a crucial concept in understanding the kinetics and dynamics of chemical reactions, including those that take place within living organisms as part of cellular metabolism and enzymatic processes.
Active site: The active site is the specific region of an enzyme where a substrate binds and catalysis takes place. It is typically a pocket or groove on the enzyme's surface.
Active Site: The active site is a specific region on an enzyme molecule where the substrate binds and the catalytic reaction takes place. It is the functional center of the enzyme that facilitates the chemical transformation of substrates into products.
Adenosine diphosphate (ADP): Adenosine diphosphate (ADP) is a nucleotide involved in energy transfer within cells. It is formed by the removal of one phosphate group from ATP and can be converted back to ATP through phosphorylation.
Adenosine monophosphate (AMP): Adenosine monophosphate (AMP) is a nucleotide composed of adenine, ribose, and one phosphate group. It plays a crucial role in cellular energy transfer and metabolism.
Adenosine triphosphate (ATP): Adenosine triphosphate (ATP) is the primary energy carrier in cells, facilitating various biochemical reactions. It consists of adenine, ribose, and three phosphate groups.
Allosteric activator: An allosteric activator is a molecule that binds to an enzyme at a site other than the active site, inducing a conformational change that enhances the enzyme's activity. This regulation mechanism is crucial for controlling metabolic pathways in microbes.
Allosteric site: An allosteric site is a specific location on an enzyme, distinct from the active site, where molecules can bind and modulate the enzyme's activity. These sites play a crucial role in regulating metabolic pathways.
Allosteric Site: An allosteric site is a location on an enzyme or protein that is distinct from the active site, where the binding of a regulatory molecule can influence the enzyme's or protein's activity and function. These sites allow for the modulation of a protein's behavior in response to changes in the cellular environment.
Anabolism: Anabolism is the set of metabolic pathways that construct molecules from smaller units, requiring energy input. It is essential for cell growth, repair, and differentiation.
Anabolism: Anabolism is the set of metabolic pathways that construct molecules from smaller, simpler precursors. It is the synthetic phase of metabolism that requires energy input to build complex organic molecules from smaller units, in contrast to the catabolic breakdown of molecules to release energy.
Apoenzyme: An apoenzyme is the protein component of an enzyme, which requires a cofactor to become fully active. Without its cofactor, an apoenzyme is inactive and unable to catalyze reactions.
ATP (Adenosine Triphosphate): ATP, or adenosine triphosphate, is the primary energy currency of the cell. It is a high-energy molecule that stores and transports chemical energy within living organisms, powering a wide range of cellular processes. ATP is central to the fundamental mechanisms of life, as it is involved in various metabolic pathways, including carbohydrate metabolism, cellular respiration, and photosynthesis.
Autotroph: An autotroph is an organism that produces its own food from inorganic substances using light or chemical energy. They are primary producers in the food chain.
Autotrophs: Autotrophs are organisms that can produce their own organic compounds, typically through the process of photosynthesis or chemosynthesis, using inorganic substances as their source of energy and nutrients. They are the foundation of many ecosystems, as they serve as the primary producers that convert energy from the environment into forms that can be used by other organisms.
Bioenergetics: Bioenergetics is the study of the energy transformations that occur within living organisms. It focuses on how cells capture, transform, and utilize energy to sustain life through various biochemical processes.
Biosynthesis: Biosynthesis is the process by which living organisms produce complex molecules from simpler ones. It involves various enzymatic reactions to build cellular components.
Catabolism: Catabolism is a metabolic pathway that breaks down molecules into smaller units, releasing energy. It involves the degradation of complex molecules such as carbohydrates, lipids, and proteins.
Catabolism: Catabolism is the set of metabolic pathways that break down molecules into smaller units, releasing energy in the process. It is the destructive phase of metabolism that provides the energy and raw materials needed for the body's essential functions and cellular processes.
Catalysis: Catalysis is the process by which a catalyst increases the rate of a chemical reaction without being consumed or altered itself. It is a fundamental concept in biochemistry and plays a crucial role in the functioning of enzymes, which are biological catalysts essential for life.
Catalyst: A catalyst is a substance that increases the rate of a chemical reaction without being consumed in the process. In biological systems, enzymes act as catalysts to facilitate metabolic reactions.
Chemoautotrophs: Chemoautotrophs are a type of microorganism that can obtain their energy by oxidizing inorganic chemical compounds, rather than relying on organic compounds or sunlight like other organisms. This allows them to serve as the primary producers in certain ecosystems, forming the base of the food chain.
Chemoheterotroph: A chemoheterotroph is an organism that derives its energy from chemical compounds and its carbon from organic sources. They rely on the consumption of other organisms or organic substances for survival.
Chemoheterotrophs: Chemoheterotrophs are a type of organism that obtain their energy and organic carbon compounds from the chemical breakdown of complex organic molecules. They rely on external sources of organic carbon, such as glucose or other organic compounds, to meet their energy and carbon needs for growth and metabolism.
Chemotroph: Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environments. These can be organic or inorganic molecules.
Coenzyme: A coenzyme is a non-protein organic molecule that binds to an enzyme and is essential for its activity. Coenzymes often act as carriers for chemical groups or electrons during enzymatic reactions.
Coenzyme A (CoA): Coenzyme A (CoA) is a molecule that plays a crucial role in the metabolism of carbohydrates, fats, and proteins. It acts as a carrier of acyl groups in various biochemical reactions.
Coenzymes: Coenzymes are organic, non-protein molecules that work in conjunction with enzymes to facilitate and enhance specific chemical reactions in the body. They serve as essential cofactors, providing the necessary components or environment for enzymes to carry out their catalytic functions effectively.
Cofactor: A cofactor is a non-protein chemical compound that is required for an enzyme's biological activity. Cofactors can be metal ions or organic molecules, often referred to as coenzymes.
Cofactors: Cofactors are non-protein chemical compounds that are required for the proper function of enzymes. They assist enzymes in catalyzing chemical reactions by providing essential components or by modifying the enzyme's structure to facilitate the reaction.
Competitive inhibitor: A competitive inhibitor is a molecule that binds to the active site of an enzyme, preventing the substrate from binding and thus inhibiting enzyme activity. This type of inhibition can be overcome by increasing the concentration of the substrate.
Competitive Inhibitors: Competitive inhibitors are substances that bind to the active site of an enzyme, preventing the substrate from accessing the enzyme and thus reducing the enzyme's activity. This type of inhibition is reversible and occurs when the inhibitor and substrate compete for the same binding site on the enzyme.
Dephosphorylation: Dephosphorylation is the removal of a phosphate group from an organic molecule by the action of enzymes. This process is crucial for regulating cellular activities and metabolic pathways.
Electron carrier: An electron carrier is a molecule that transports electrons during cellular respiration and photosynthesis. They play a crucial role in the transfer of energy within cells.
Electron Transport Chains: Electron transport chains are a series of proteins and electron carriers embedded in the inner membrane of mitochondria that facilitate the transfer of electrons from one molecule to another, ultimately driving the production of ATP through the process of oxidative phosphorylation. These chains are essential for the efficient conversion of energy stored in organic molecules into a usable form, ATP, which powers various cellular processes.
Endergonic reaction: An endergonic reaction is a chemical reaction that requires an input of energy to proceed. These reactions are non-spontaneous and have a positive Gibbs free energy change.
Enthalpy: Enthalpy is a thermodynamic property that represents the total energy of a system, including its internal energy and the work done by or on the system due to changes in pressure and volume. It is a crucial concept in understanding the energy changes that occur during chemical reactions and physical processes.
Entropy: Entropy is a measure of the disorder or randomness of a system. It represents the unavailability of a system's thermal energy for conversion into work, often interpreted as the degree of disorder or uncertainty in a system. Entropy is a fundamental concept in thermodynamics, information theory, and other scientific fields, and it plays a crucial role in understanding the behavior of energy, matter, and enzymes.
Enzyme: An enzyme is a biological catalyst that speeds up chemical reactions in cells without being consumed. They are essential for metabolic processes.
Enzyme Kinetics: Enzyme kinetics is the study of the rates and mechanisms of chemical reactions catalyzed by enzymes. It provides insights into how enzymes function and how their activity can be modulated to influence biological processes.
Escherichia coli: Escherichia coli (E. coli) is a Gram-negative, rod-shaped bacterium commonly found in the intestines of warm-blooded organisms. While most strains are harmless, some can cause serious food poisoning and infections.
Exergonic reaction: An exergonic reaction is a chemical reaction that releases energy by breaking down complex molecules into simpler ones. It often involves the release of heat and increases the entropy of the system.
FAD: FAD (Flavin Adenine Dinucleotide) is a redox-active coenzyme involved in several important metabolic reactions. It functions as an electron carrier in cellular respiration and other biochemical pathways.
FADH2: FADH2 is a reduced form of flavin adenine dinucleotide, a coenzyme involved in various metabolic processes. It plays a crucial role in the electron transport chain and cellular respiration.
Feedback inhibition: Feedback inhibition is a regulatory mechanism in which the end product of a metabolic pathway inhibits an enzyme involved earlier in the pathway. This prevents the overproduction of the product and helps maintain metabolic balance.
Flavin adenine dinucleotide: Flavin adenine dinucleotide (FAD) is a redox-active coenzyme associated with various proteins. It plays a crucial role in metabolism by acting as an electron carrier in the electron transport chain.
Glycolysis: Glycolysis is the metabolic pathway that converts glucose, a six-carbon sugar, into two molecules of pyruvate, a three-carbon compound. This process is the first stage of cellular respiration and occurs in the cytoplasm of cells, providing a crucial source of energy for the cell.
Heterotroph: A heterotroph is an organism that cannot synthesize its own food and relies on complex organic substances for nutrition. Heterotrophs obtain their energy by consuming other organisms or organic matter.
Heterotrophs: Heterotrophs are organisms that obtain their energy and organic compounds from other living things, as they are unable to produce their own food through photosynthesis or chemosynthesis. They rely on the consumption of organic compounds, such as carbohydrates, lipids, and proteins, produced by other organisms.
High-energy phosphate bond: A high-energy phosphate bond is a type of chemical bond found in molecules like ATP (adenosine triphosphate) that stores and releases a significant amount of energy during hydrolysis. These bonds are crucial for various biological processes, including muscle contraction and cellular metabolism.
Holoenzyme: A holoenzyme is a biochemically active enzyme complex that includes both an apoenzyme (protein portion) and its necessary cofactor(s), which can be either metal ions or organic molecules. It is the fully functional form of the enzyme, capable of catalyzing reactions.
Induced fit: Induced fit is a model describing how enzymes change shape to accommodate the substrate, enhancing the enzyme's ability to catalyze the reaction. This dynamic adjustment increases specificity and efficiency in biochemical reactions.
Inorganic phosphate [Pi]: Inorganic phosphate (Pi) is a simple phosphate ion, essential for cellular energy transfer. It plays a critical role in microbial metabolism, particularly in ATP synthesis and degradation.
Krebs Cycle: The Krebs cycle, also known as the citric acid cycle or tricarboxylic acid (TCA) cycle, is a series of chemical reactions that occur in the mitochondria of cells. It is a key part of cellular respiration, which is the process of converting the chemical energy stored in organic molecules, such as glucose, into a form that can be used by the cell, known as adenosine triphosphate (ATP).
Lithotroph: Lithotrophs are microorganisms that obtain energy by oxidizing inorganic compounds. They play a crucial role in various biogeochemical cycles.
Metabolic pathway: A metabolic pathway is a series of enzymatically catalyzed chemical reactions within a cell that lead to the conversion of substrates into products. These pathways are crucial for cellular processes such as energy production and biosynthesis.
Metabolism: Metabolism is the set of life-sustaining chemical reactions in organisms. It involves pathways for both breaking down molecules to obtain energy (catabolism) and building up molecules necessary for cellular function (anabolism).
Metabolism: Metabolism is the sum of all the chemical reactions that occur within an organism to sustain life. It involves the breakdown of complex molecules for energy (catabolism) and the synthesis of complex molecules from simpler ones (anabolism). Metabolism is a crucial aspect of both the unique characteristics of prokaryotic cells and the role of energy, matter, and enzymes in biological systems.
Michaelis Constant: The Michaelis constant is a measure of the affinity between an enzyme and its substrate, representing the substrate concentration at which the reaction rate is half the maximum rate. It is a crucial parameter in understanding enzyme kinetics and the efficiency of enzymatic reactions.
NAD+: NAD+, or nicotinamide adenine dinucleotide, is a coenzyme found in all living cells. It is essential for numerous metabolic processes, serving as an electron carrier in redox reactions that are crucial for energy production and various other cellular functions.
NAD+/NADH: NAD+ (Nicotinamide adenine dinucleotide) is a coenzyme central to metabolism, acting as an electron carrier. NADH is the reduced form of NAD+ after it has accepted electrons.
NADP+: NADP+ (Nicotinamide adenine dinucleotide phosphate) is a coenzyme that functions as an electron carrier in various biochemical reactions. It plays a crucial role in anabolic reactions, such as photosynthesis and lipid synthesis.
NADPH: NADPH (Nicotinamide Adenine Dinucleotide Phosphate) is a coenzyme that plays a crucial role in anabolic reactions and photosynthesis. It acts as a reducing agent, donating electrons and hydrogen to various biochemical reactions.
Nicotinamide adenine dinucleotide: Nicotinamide adenine dinucleotide (NAD+) is a coenzyme found in all living cells. It plays a crucial role in redox reactions, carrying electrons from one reaction to another.
Nicotine adenine dinucleotide phosphate: Nicotinamide adenine dinucleotide phosphate (NADP) is a coenzyme that functions as an electron carrier in various biochemical reactions. It plays a vital role in anabolic reactions, such as fatty acid and nucleic acid synthesis.
Noncompetitive (allosteric) inhibitor: A noncompetitive (allosteric) inhibitor binds to an enzyme at a site other than the active site, causing a conformational change that reduces the enzyme's activity. This type of inhibition is not overcome by increasing substrate concentration.
Noncompetitive Inhibitors: Noncompetitive inhibitors are a type of enzyme inhibitor that bind to a site on the enzyme that is distinct from the active site, causing a conformational change that reduces the enzyme's activity. Unlike competitive inhibitors, noncompetitive inhibitors do not compete with the substrate for the active site.
Organotroph: An organotroph is an organism that obtains electrons or hydrogen atoms from organic compounds to fuel its metabolic processes. These organisms rely on organic molecules as their electron donors for energy production.
Oxidation reaction: An oxidation reaction involves the loss of electrons from a molecule, atom, or ion. In microbial metabolism, these reactions are essential for energy production.
Oxidation-Reduction: Oxidation-reduction, or redox, is a fundamental chemical process that involves the transfer of electrons between atoms or molecules. It is a key concept in understanding energy transformations and the functioning of enzymes within living organisms.
Phosphate group: A phosphate group is a molecule consisting of one phosphorus atom bonded to four oxygen atoms. It plays a crucial role in energy transfer and storage within cells.
Phosphorylation: Phosphorylation is the process of adding a phosphate group to a molecule, often mediated by enzymes. It plays a crucial role in cellular signaling and energy transfer.
Photoautotrophs: Photoautotrophs are organisms that can synthesize their own organic compounds from inorganic carbon sources, such as carbon dioxide, using energy from sunlight through the process of photosynthesis. This ability to produce their own food from light energy and carbon dioxide is a key feature of photoautotrophs and connects them to the topics of energy, matter, and environmental conditions that affect growth.
Photosynthesis: Photosynthesis is a biochemical process by which phototrophic organisms convert light energy into chemical energy, storing it in the bonds of glucose molecules. This process primarily occurs in chlorophyll-containing cells and involves both light-dependent and light-independent reactions.
Phototroph: Phototrophs are organisms that obtain energy from light to synthesize organic compounds. They play a crucial role in converting solar energy into chemical energy.
Pyrophosphate [PPi]: Pyrophosphate (PPi) is a byproduct of many biochemical reactions, particularly those involving ATP hydrolysis. It plays a crucial role in energy metabolism and enzyme regulation.
Redox: Redox, short for reduction-oxidation, is a fundamental chemical process that involves the transfer of electrons between chemical species. This process is central to the concepts of energy, matter, and enzyme function in biological systems.
Redox reaction: A redox reaction is a chemical process involving the transfer of electrons between two substances. It consists of two parts: oxidation, where a substance loses electrons, and reduction, where a substance gains electrons.
Reduction reaction: A reduction reaction is a chemical process in which a molecule, atom, or ion gains electrons. This process often leads to a decrease in oxidation state and is essential in various metabolic pathways.
Substrate: A substrate is the specific reactant that an enzyme acts upon during a biochemical reaction. It binds to the enzyme's active site, facilitating a chemical transformation.
Sulfa drug: Sulfa drugs are a group of synthetic antimicrobial agents that contain the sulfonamide group. They inhibit bacterial growth by interfering with the synthesis of folic acid.
Thermodynamics: Thermodynamics is the branch of physics that deals with the relationship between heat, work, temperature, and energy. It describes the transfer of energy as it relates to the physical and chemical changes that occur in a system.