Microbial Metabolism Lecture Flashcards

Metabolism: Definition and Overview

• Metabolism: This term encompasses all chemical and physical workings of a cell. It is the sum of all chemical reactions occurring within the organism.

• Types of Chemical Reactions:

  • Catabolism: A degradative process that breaks the bonds of larger molecules into smaller molecules. This process is energy-yielding, meaning it releases energy to the cell.

  • Anabolism: A biosynthetic process that forms larger macromolecules from smaller precursor molecules. This process requires an input of energy.

• Energy and Substrate Cycling:

  • Nutrients: Act as sources of energy (carbohydrates, lipids, proteins) and building blocks.

  • Catabolic Pathway: Energy release from nutrients (carbohydrates, lipids, proteins) produces $ATP$ and $NADH$. It results in end products with reduced energy, such as $CO_2$ and $H_2O$.

  • Anabolic Pathway: Uses $ATP$ and energetic carriers to synthesize complex cell structures (carbohydrates, proteins, lipids) from simple building blocks like sugars and amino acids.

Enzymes: Biological Catalysts

• Fundamental Role: Enzymes are biological catalysts that increase the rate of chemical reactions specifically by lowering the energy of activation (defined as the resistance to a reaction).

• Properties of Enzymes:

  • They are not permanently altered or consumed during the reaction.

  • They promote reactions by serving as physical sites where specific substrate molecules can interact.

• Energy State of Reactions:

  • The energy of activation is significantly higher in the absence of an enzyme compared to when an enzyme is present.

  • The reaction progresses from the Initial State (Reactants) to the Final State (Products).

Enzyme Structure and Classification

• Simple Enzymes: Consist solely of protein molecules.

• Conjugated Enzymes (Holoenzymes): Contain both protein and nonprotein components.

  • Apoenzyme: The protein portion of the holoenzyme.

  • Cofactors: The nonprotein portion.

    • Inorganic Elements (Metal Ions): Examples include iron, copper, and magnesium.

    • Organic Molecules (Coenzymes): Often derived from vitamins.

Specific Examples of Enzymes and Their Cofactors

• Catalase: Breaks down hydrogen peroxide; requires Iron ($Fe$).

• Oxidase: Adds electrons to oxygen; requires Iron ($Fe$) and Copper ($Cu$).

• Hexokinase: Transfers phosphate to glucose; requires Magnesium ($Mg$).

• Arginase: Acts on the amino acid arginine; requires Manganese ($Mn$).

• Nitrate Reductase: Reduces nitrate to nitrite; requires Molybdenum ($Mo$).

• DNA Polymerase: Synthesis of DNA; requires Zinc ($Zn$) and Magnesium ($Mg$).

• Botulinum Toxin: Hydrolyzes protein needed for vesicle transport; requires Zinc ($Zn$).

• Pyruvate Dehydrogenase: Converts pyruvic acid to acetyl $CoA$ and $CO_2$; requires Thiamine and Magnesium ($Mg$).

• Succinate Dehydrogenase: Oxidizes succinate to fumarate in the Krebs cycle; requires $FAD$ (contains riboflavin).

Apoenzymes: Specificity and the Active Site

• Organizational Levels: Apoenzymes exhibit primary, secondary, and tertiary protein organization.

• Quaternary Structure: Larger, more complex enzymes exhibit a quaternary structure, which consists of more than one polypeptide chain.

• Active Site (Catalytic Site): The specific region of the enzyme where the substrate binds.

• Structural Formation:

  • As the polypeptide forms intrachain bonds and folds, it assumes a three-dimensional tertiary state displaying the active site ($AS$).

  • Because every polypeptide folds uniquely, each apoenzyme has a uniquely shaped active site.

  • In complex enzymes, new active sites may form at the junction of multiple polypeptides.

Enzyme-Substrate Interactions

• Induced Fit: A temporary enzyme-substrate union occurrs when a substrate moves into the active site. The enzyme changes shape slightly to fit the substrate more securely.

• Result: Following the interaction, the appropriate reaction occurs, and the product is released. The enzyme remains unchanged and ready for the next substrate.

The Function of Cofactors and Coenzymes

• Metallic Cofactors (Metal Ions):

  • Activate enzymes.

  • Participate in bringing the active site and substrate into proximity.

  • Engage directly in chemical reactions with the enzyme-substrate complex.

• Coenzymes (Organic Factors):

  • Serve as temporary carriers for specific substrates.

  • Vitamins are the most common source of coenzymes.

• Mechanism of Coenzyme Action:

  1. The enzyme and coenzyme position themselves to react with two substrates.

  2. The coenzyme removes a chemical group from Substrate 1.

  3. The coenzyme readies the chemical group for transfer to Substrate 2.

  4. The group is bound to Substrate 2, and the altered substrates are released.

Classification and Naming of Enzymes

• Enzymes are classified by site of action, type of action, and substrate.

• Sampling of Enzymes:

  • Lactase: Substrate: Lactose. Action: Breaks lactose into glucose and galactose.

  • Penicillinase: Substrate: Penicillin. Action: Hydrolyzes the beta-lactam ring.

  • DNA Polymerase: Substrates: DNA nucleotides. Action: Synthesizes DNA strands using a complementary model.

  • Lactate Dehydrogenase: Substrate: Pyruvic acid. Action: Converts pyruvic acid to lactic acid.

  • Oxidase: Substrate: Molecular oxygen ($O_2$). Action: Catalyzes the reduction (addition of electrons and hydrogen ions) to $O_2$.

Localization and Regularity of Enzyme Action

• Location:

  • Exoenzymes: Transported extracellularly to break down large food molecules (e.g., cellulase, amylase) or harmful chemicals (e.g., penicillinase).

  • Endoenzymes: Retained and function intracellularly. Most metabolic enzymes fall into this category.

• Regularity:

  • Constitutive Enzymes: Always present and produced at equal rates regardless of substrate amount.

  • Regulated Enzymes: Production is induced (turned on) or repressed (turned off) in response to substrate concentration changes.

Synthesis and Hydrolysis Reactions

• Synthesis (Condensation/Dehydration Reactions):

  • Anabolic reactions that build large substrates from smaller ones.

  • They release one water ($H_2O$) molecule for every bond formed.

  • Example: Forming a glycosidic bond between two glucose molecules to make maltose.

• Hydrolysis Reactions:

  • Catabolic reactions that break large substrates into smaller molecules.

  • They require the input of water to break the bonds.

  • Example: Breaking a peptide bond between amino acids by adding $OH$ to one and $H$ to the other.

Environmental Sensitivity

• Enzymes operate under specific temperature, $pH$, and osmotic pressure conditions dictated by the organism's habitat.

• Labile: Chemically unstable enzymes due to environmental changes.

• Denaturation: The breaking of weak bonds that maintain the native shape of the apoenzyme, leading to loss of function.

Regulation of Metabolic Pathways

• Metabolic pathways are multienzyme systems that proceed in a stepwise, regulated manner to maximize nutrient/energy use.

• Patterns of Pathways:

  • Linear: A simple sequence ($A \rightarrow B \rightarrow C \rightarrow D$).

  • Cyclic: The starting molecule is regenerated at the end.

  • Divergent: One pathway splits into two.

  • Branched: Pathways that lead to different end products.

  • Convergent: Different pathways lead to the same intermediate or product.

Direct Controls on Enzyme Action

• Competitive Inhibition: A substance mimicking the substrate competes for the active site.

• Allosteric Inhibition: A type of competitive inhibition where an enzyme has two sites: the active site and the regulatory (allosteric) site. Negative feedback occurs when a product binds to the regulatory site.

• Noncompetitive Inhibition: The inhibitor binds to the entire enzyme-substrate complex, halting the reaction.

Genetic Control of Enzyme Synthesis

• Enzyme Repression: Automatic suppression of enzyme synthesis when the end product builds up to excess. The product binds to DNA to shut down production. Response is slow but enduring.

• Enzyme Induction: Enzymes are synthesized only when suitable substrates are present, allowing adaptation to nutrients and preventing energy waste.

Cell Energetics and ATP

• Energy: The capacity to do work. Forms include thermal, radiant, electrical, mechanical, atomic, and chemical.

• Reaction Types:

  • Endergonic: Consumes energy ($Energy + A + B \xrightarrow{\text{Enzyme}} C$).

  • Exergonic: Releases energy ($X + Y \xrightarrow{\text{Enzyme}} Z + Energy$).

• Biological Redox Reactions:

  • Occur in pairs (Redox pair: electron donor and acceptor).

  • Energy released during electron transfer is often used to phosphorylate $ADP$.

• Electron Carriers: Molecules like $NAD^+$, $FAD$, and Coenzyme A facilitate energy transfer.

  • Redox of NAD: $NAD^+ + 2H^+ + 2e^- \rightleftharpoons NADH + H^+$.

Structure and Role of ATP

• ATP (Adenosine Triphosphate): The "metabolic currency."

  • Composition: Adenine (nitrogenous base), Ribose (5-carbon sugar), and 3 Phosphate groups.

  • Energy Release: Breaking the terminal phosphate bond releases energy, converting $ATP$ to $ADP$.

• Utilization: Powers mechanical work, transport work, and chemical work (e.g., Hexokinase phosphorylating glucose into Glucose-6-phosphate).

• Mechanism of Synthesis:

  1. Substrate-level phosphorylation: Direct transfer of phosphate from a substrate to $ADP$.

  2. Oxidative phosphorylation: Series of redox reactions in the respiratory pathway.

  3. Photophosphorylation: Driven by sunlight in photosynthetic organisms.

Bioenergetics and Catabolic Strategies

• Primary Catabolism (Glucose): Processed via Glycolysis, Krebs Cycle, and the Respiratory Chain (Electron Transport System).

• Metabolic Strategies:

  1. Aerobic Respiration: Oxygen ($O_2$) is the final electron acceptor. Theoretical yield: $38$ $ATP$.

  2. Anaerobic Respiration: Utilizes oxygen-containing ions (e.g., $NO_3^-$, $SO_4^{2-}$, $CO_3^{2-}$) as final acceptors instead of free oxygen.

  3. Fermentation: Incomplete oxidation of glucose in the absence of oxygen. Organic compounds (e.g., pyruvate, acetaldehyde) are final acceptors. Maximum yield: $2$ $ATP$.

Steps of Aerobic Respiration

1. Glycolysis: Glucose ($6C$) is oxidized and split into two pyruvic acid ($3C$) molecules; yields 2 $ATP$ (net) and 2 $NADH$.

2. Krebs Cycle (TCA Cycle):

   • Linking step: Pyruvic acid is converted to Acetyl $CoA$, yielding $CO_2$ and $NADH$.

   • Step 1: $2C$ Acetyl $CoA$ + oxaloacetate yields $6C$ citrate.

   • Step 3: Isocitrate yields $5C$ $\alpha$-ketoglutarate, $NADH$, and $CO_2$.

   • Step 4: $\alpha$-ketoglutarate yields $4C$ succinyl $CoA$, $NADH$, and $CO_2$.

   • Step 5: Succinyl $CoA$ becomes succinate; produces 1 $ATP$.

   • Step 6: Succinate becomes fumarate; yields $FADH_2$.

   • Step 8: Malate becomes oxaloacetate; yields $NADH$.

3. Electron Transport System (ETS):

   • Reduced carriers ($NADH$, $FADH_2$) transfer electrons to a chain of redox carriers (NAD dehydrogenase, $CoQ$, Cytochromes).

   • Chemiosmosis: Electrons flowing through the ETS trigger the pumping of hydrogen ions (protons) across the membrane, creating a proton motive force.

   • ATP Synthase: Protons diffuse back through the $F_o$ portion, causing the $F_1$ portion to rotate and synthesize $ATP$ from $ADP$ and $P_i$. Each $ATP$ requires 3 protons.

   • Terminal Reaction: $2H^+ + 2e^- + \frac{1}{2} O_2 \rightarrow H_2O$.

Summary of Aerobic Respiration Stoichiometry

• Overall Reaction: $C_6H_{12}O_6 + 6O_2 + 38ADP + 38P_i \rightarrow 6CO_2 + 6H_2O + 38ATP$.

• ATP Breakdown:

  • Glycolysis: 2 $ATP$.

  • Krebs Cycle: 2 $ATP$.

  • Electron Transport: 34 $ATP$.

Fermentation Specifics

• Alcoholic Fermentation: Used by yeasts; converts pyruvic acid to acetaldehyde, then to ethyl alcohol while releasing $CO_2$.

• Acidic Fermentation:

  • Homolactic: Pyruvic acid reduced to lactic acid (e.g., in human muscle or bacteria).

  • Mixed Acid: Production of acetic, lactic, succinic, and formic acids, along with $CO_2$ and $H_2$ gas (e.g., Escherichia, Shigella).

  • Other Products: 2,3-butanediol (Enterobacter), Propionic acid (Propionibacterium), Butyric acid (Clostridium).

Biosynthesis and Amphibolic Pathways

• Amphibolic: Pathways that serve both catabolic and anabolic functions.

• Intermediates and Diversion:

  • Ammination: Pyruvic acid converted to amino acids.

  • Deamination: Amino acids converted to energy sources (removing the amino group).

  • Transamination: Exchange of amino groups between amino acids and keto acids.

  • Glyceraldehyde-3-phosphate serves as a precursor for amino acids, carbohydrates, and fats.

Photosynthesis: Mechanism and Stages

• Global Impact: 80%-90% of photosynthesis is aquatic (algae, cyanobacteria).

• Equation: $6CO_2 + 6H_2O \xrightarrow{\text{Light and Pigment}} C_6H_{12}O_6 + 6O_2$.

• Light-Dependent Reactions:

  • Occur in thylakoid membranes.

  • Photons are absorbed by chlorophyll (comprised of a porphyrin head and hydrocarbon tail).

  • Photolysis: Water is split, releasing $O_2$ and electrons.

  • Produces $ATP$ and $NADPH$.

• Light-Independent Reactions (Calvin Cycle):

  • Occurs in the stroma.

  • Carbon Fixation: $CO_2$ is fixed to ribulose-1,5-bisphosphate ($RuBP$).

  • Use of $ATP$ and $NADPH$ to reduce intermediates into glucose and other organic molecules.

  • Regeneration of $RuBP$ allows the cycle to continue.