Metabolism and Enzyme Regulation Vocabulary

Enzyme Structure and Nomenclature

• Enzymatic Nomenclature:

  • Enzymes are typically identified by the suffix "-ase" at the end of their name.

• Chemical Composition of Enzymes:

  • Some enzymes consist $100\%$ of protein.

  • Other enzymes consist of a protein component and a non-protein component:

  • Apoenzyme: The protein portion of a complex enzyme.

  • Cofactor: The non-protein portion required for enzyme function.

  • Holoenzyme: Formed when an apoenzyme combines with an inorganic cofactor (such as calcium or iron).

  • Coenzyme: Formed when the cofactor associated with the apoenzyme is organic.

• Active Site and Specificity:

  • Active Site: The specific location on the enzyme where the catalytic reaction takes place and where the substrate binds.

  • High Specificity: Enzymes are highly specific and only interact with particular substrates.

  • Catalytic Mechanism: Enzymes function as biological catalysts by lowering the activation energy required for a chemical reaction to occur, thereby increasing the reaction rate.

• Enzyme Turnover Number:

  • The turnover number represents the maximum number of substrate molecules an enzyme converts to products each second.

  • Turnover rates vary depending on the enzyme, typically ranging from $1,000$ to $10,000$ conversions per second, with some enzymes exhibiting even higher rates.

Enzyme Classification and Production Dynamics

• Spatial Classification of Enzymes:

  • Endoenzymes: Enzymes manufactured inside the cell that remain and function internally (e.g., metabolic enzymes).

  • Exoenzymes: Enzymes manufactured inside the cell that are secreted across the cell membrane to function externally (e.g., defense enzymes).

• Regulation of Enzyme Synthesis:

  • Constitutive Enzymes: Enzymes that are continuously produced by the cell at a constant rate regardless of environmental changes.

  • Example: Enzymes required for glucose metabolism are constitutive because glucose serves as the primary and preferred nutrient source for many bacteria.

  • Induced Enzymes: Enzymes produced only when their specific substrate is present in the environment and needed by the cell.

  • Example: If glucose is depleted from the environment and lactose becomes available, the enzymes required for lactose breakdown are induced (manufactured). When glucose is replenished, the cell reverts to utilizing glucose, and the synthesis of lactose-metabolizing enzymes is shut off.

Biochemical Reactions and Coenzyme Function

• Types of Metabolic Reactions:

  • Catabolic Reactions: Decomposition reactions involving the breakdown of larger substrates into smaller, simpler products.

  • Anabolic Reactions: Synthesis reactions in which smaller subunits are linked together to build complex macromolecules.

• Reduction-Oxidation (Redox) Reactions:

  • Oxidation: The loss of one or more electrons from a molecule.

  • Reduction: The gain of one or more electrons by a molecule.

  • Coupling: Oxidation and reduction reactions always occur simultaneously as coupled redox reactions; whenever one substance is oxidized, another is reduced.

  • Charge Transfer: The movement of negative charges (electrons) is accompanied by positive charges, typically in the form of hydrogen ions ($H^+$).

• Coenzyme Function - Nicotinamide ($NAD$):

  • Nicotinamide Adenine Dinucleotide ($NAD$) is a coenzyme containing an organic cofactor.

  • Acts as a primary electron carrier during metabolic charge transfers.

  • Exists in an oxidized state ($NAD^+$) and a reduced state ($NADH + H^+$).

Factors Affecting Enzyme Activity and Regulation

• Factors Influencing Enzyme Activity:

  • Temperature: Excessively high temperatures disrupt the hydrogen bonds maintaining the enzyme's three-dimensional shape, causing denaturation. Denaturation linearizes the protein, rendering the enzyme non-functional.

  • pH: Alterations in pH levels can induce conformational changes or denaturation, diminishing enzyme activity.

  • Substrate Concentration: Increasing substrate concentration increases reaction velocity until a saturation point is reached. Once all enzyme active sites are occupied by substrate, adding additional substrate will not increase the turnover rate.

• Enzyme Inhibition Mechanisms:

  • Need for Regulation: Prevents the overaccumulation of metabolic end-products within the cell, allowing the cell to consume existing products before producing more.

  • Competitive Inhibition:

  • An inhibitor molecule binds directly to the active site of the enzyme.

  • Mechanically blocks the active site, preventing substrate binding and catalytic conversion.

  • Reversible Nature: Once the cell consumes excess product, the inhibitor detaches from the active site, allowing normal substrate binding to resume.

  • Non-Competitive Inhibition:

  • An inhibitor binds to a secondary site on the enzyme known as the allosteric site (a site distinct from the active site that plays no role in standard substrate breakdown).

  • Binding occurs via strong covalent bonds.

  • Induces a conformational change in the enzyme that alters the shape of the active site so that the substrate can no longer fit.

  • Irreversible Nature: In most cases, non-competitive inhibition is permanent, permanently deactivating the enzyme's catalytic capabilities.

  • Feedback Inhibition: A regulatory loop in which accumulated excess product acts as an inhibitor to turn down enzyme activity early in a pathway.

Ribozymes

• Composition and Nature:

  • Ribozymes are catalytic molecules composed entirely of RNA (ribonucleic acid) rather than protein.

• Function:

  • Possess catalytic activity and play a critical functional role in protein synthesis (translation).

Fundamentals of Cellular Respiration and ATP

• Aerobic vs. Anaerobic Respiration:

  • Respiration/Metabolism occurs under both aerobic and anaerobic conditions.

  • Aerobic Respiration: Oxygen ($O_2$) serves as the final or terminal electron acceptor at the end of the electron transport process.

  • Anaerobic Respiration: An inorganic compound other than oxygen (e.g., iron or sulfur) serves as the terminal electron acceptor.

• Adenosine Triphosphate ($ATP$) Energy Dynamics:

  • ATP is a high-energy, unstable molecule that acts as the primary energy currency of the cell.

  • Energy Release: Removal of the terminal phosphate group via a hydrolysis reaction (the addition of water to cleave the bond) releases stored energy, converting ATP to adenosine diphosphate ($ADP$).

• Modes of Phosphorylation (ADP to ATP Conversion):

  • Oxidative Phosphorylation: Highly efficient process occurring under both aerobic and anaerobic conditions that breaks down glucose or other organic molecules.

  • Photophosphorylation: Highly efficient process driven by light energy, occurring in both aerobic and anaerobic environments.

  • Substrate-Level Phosphorylation (Fermentation): Incomplete breakdown of substrates, predominantly occurring under anaerobic conditions (though possible in oxygen presence); less efficient, requiring higher frequency to meet cellular energy demands.

Glycolysis

• Pathway Overview:

  • Represents the initial preparatory phase in the breakdown of glucose.

  • Substrate: Starts with one $6$-carbon glucose molecule.

  • Product: Yields two $3$-carbon pyruvate molecules.

  • Lysis: "Glycolysis" denotes the splitting ("lysis") of sugar ("glyco").

• Cellular Localization:

  • Prokaryotes: Takes place in the cytoplasm.

  • Eukaryotes: Takes place in the cytoplasm.

• Energetics:

  • Active transport of nutrients into the cell requires an initial expenditure of cellular ATP.

  • Glycolysis itself consumes some ATP during its initial steps and yields no major generation of ATP; it serves primarily to prepare molecules for downstream cyclic reactions.

The Krebs Cycle (Tricarboxylic Acid Cycle)

• Cellular Localization:

  • Prokaryotes: Occurs in the cytoplasm.

  • Eukaryotes: Occurs in the mitochondrial matrix.

• Preparatory Phase (Transition Step):

  • Pyruvate cannot directly enter the cyclic portion of the pathway and must undergo modification:

  • Decarboxylation: Removal of carbon dioxide ($CO_2$) converts $3$-carbon pyruvate into a $2$-carbon acetyl group.

  • Reduction: Simultaneously, $NAD^+$ is reduced to $NADH + H^+$ during this step.

  • Coenzyme A Transport: Coenzyme A binds to the acetyl group to form acetyl coenzyme A (acetyl-CoA), which shuttles acetyl into the cyclic pathway. Coenzyme A is subsequently released and recycled.

• Cyclic Pathway Steps:

  • Condensation: The $2$-carbon acetyl group combines with a $4$-carbon oxaloacetate molecule to form a $6$-carbon citrate molecule.

  • Continuous Decarboxylation: Carbon dioxide ($CO_2$) is repeatedly cleaved off during the cycle.

  • Coenzyme Reduction: High amounts of electron carriers are reduced, generating reduced nicotinamide adenine dinucleotide ($NADH$) and reduced flavin adenine dinucleotide ($FADH_2$).

  • Guanosine Triphosphate Production: Substrate-level phosphorylation yields GTP through the addition of a phosphate group to GDP.

• Stoichiometry and Outputs:

  • Because one glucose molecule yields two pyruvate molecules during glycolysis, the Krebs cycle turns $2$ times per glucose molecule metabolized.

  • Primary Result: Production of abundant reduced coenzymes ($NADH$ and $FADH_2$) and release of $CO_2$ byproduct.

The Electron Transport Chain

• Cellular Localization:

  • Prokaryotes: Embedded along the cytoplasmic membrane.

  • Eukaryotes: Embedded along the inner mitochondrial membrane.

• Biochemical Function:

  • Consists of a sequence of membrane-bound carrier molecules that undergo a series of redox reactions.

  • Oxidizes the reduced coenzymes ($NADH$ and $FADH_2$) generated in the Krebs cycle by stripping them of electrons and hydrogen ions ($H^+$).

  • Glucose breakdown is complete by this stage; the chain operates exclusively on reduced coenzymes.

• Classes of Carrier Molecules:

  • Flavoproteins: Proteins containing flavin (a derivative of vitamin B12).

  • Cytochromes: Iron-containing proteins that undergo electron transfer.

  • Coenzyme Q: A non-protein organic electron carrier.

• Electron Transfer and Terminal Acceptance:

  • Electrons are passed sequentially down the chain of carrier molecules.

  • Aerobic Conditions: Oxygen ($O_2$) acts as the terminal electron acceptor, combining with electrons and protons ($H^+$) to form water ($H_2O$).

  • Anaerobic Conditions: Non-oxygen molecules (such as iron or sulfur compounds) act as terminal electron acceptors, yielding products such as acidic byproducts.

Chemiosmosis and Total ATP Yield

• Mechanism of Chemiosmosis:

  • Proton Pumping: As electrons move through the transport chain, proton pumps actively transport stripped hydrogen ions ($H^+$) across the membrane against their concentration gradient.

  • Proton Accumulation Sites:

  • Eukaryotes: $H^+$ accumulates in the cristae / intermembrane space of the mitochondrion.

  • Prokaryotes: $H^+$ accumulates in the periplasmic space (the space located between the cytoplasmic membrane and the cell wall).

  • Proton Motive Force: The high concentration of accumulated $H^+$ creates an electrochemical and pH gradient across the membrane termed the proton motive force.

• ATP Synthesis via Diffusion:

  • Passive Flow: To restore equilibrium, $H^+$ ions pass back across the membrane down their concentration gradient through embedded transmembrane proteins.

  • ATP Synthase: The transmembrane protein channel contains the enzyme ATP synthase. The flow of $H^+$ through the channel activates ATP synthase, which phosphorylates ADP into ATP.

• Overall ATP Yield Per Glucose Molecule:

  • Eukaryotes: Produces a net total of $36$ ATP molecules per glucose molecule.

  • Prokaryotes: Produces a net total of $38$ ATP molecules per glucose molecule (demonstrating greater efficiency).

Fermentation Pathways

• Characteristics of Fermentation:

  • An alternative metabolic pathway that operates with or without oxygen.

  • Bypasses both the Krebs cycle and the electron transport chain.

  • Results in incomplete breakdown of the primary substrate, yielding significantly less ATP compared to oxidative phosphorylation.

  • Uses an organic molecule as the final electron acceptor.

  • Must occur continuously at high rates to satisfy cellular energy needs.

• Major Pathways:

  • Lactic Acid Fermentation.

  • Alcohol Fermentation.