Metabolism and Enzyme Activity Study Notes

Chapter 5: Metabolism, Part 1

Introduction to Metabolism

• Definition of metabolism:

  • Metabolism refers to the collection of controlled biochemical reactions that take place within a cell.

  • All chemistry that occurs within the cell collectively known as metabolism.

  • Cells are described as bags of chemistry, with numerous reactions happening simultaneously.

Components of Metabolism

• Metabolism is divided into two main categories:

  • Catabolism:

  • Definition: Catabolism involves the breakdown of food to release energy.

  • Example: When consuming food such as a sandwich, macromolecules (proteins, lipids, carbohydrates, nucleic acids) are broken down.

  • Process: Involves breaking chemical bonds and releasing energy, typically through exergonic reactions.

  • Anabolism:

  • Definition: Anabolism refers to the building and synthesizing of cellular components from the products of catabolism.

  • Example: Using energy and parts from broken down macromolecules to create new cellular components.

  • Process: Generally involves endergonic reactions (requiring energy).

• Metabolism as a Combination:

  • Metabolism encompasses both catabolic and anabolic reactions, and these reactions occur simultaneously within cells.

Energy Dynamics in Metabolism

• Energy Harvesting from Catabolism:

  • Energy is harvested from catabolic reactions, a portion of which is lost as heat.

  • The primary energy currency in the cell is ATP (adenosine triphosphate), which is utilized for energy in anabolic processes.

Enzymes in Metabolism

• Role of Enzymes:

  • Enzymes are biological catalysts that speed up chemical reactions in cells.

  • Reactions typically occur through a pathway consisting of several enzyme-mediated steps.

• Activation Energy:

  • Definition: Activation energy is the energy required to trigger a reaction.

  • Enzymes lower the activation energy, facilitating quicker reactions.

• Substrates:

  • Definition: A substrate is the reactant in an enzymatic reaction.

  • Example: The product from the prior reaction becomes the substrate for the next step in the pathway.

Metabolic Pathways

• Metabolic Pathways:

  • Pathways consist of various reactions leading from one substrate to another, each requiring a specific enzyme.

  • Example: If an enzyme in the pathway is absent or not functioning, progression through the pathway stalls, illustrating the dependency on each enzyme's presence.

Types of Enzymes Commonly Found in Metabolism

• Isomerases:

  • Definition: Enzymes that rearrange atoms within a compound, producing isomers.

  • Example: Moving a hydroxyl (OH) group from one carbon to another.

• Transferases:

  • Definition: Enzymes that transfer functional groups (e.g., phosphate, hydroxyl) between molecules.

• Dehydrogenases:

  • Also known as oxidoreductases, are involved in redox reactions, transferring electrons often in the form of hydrogens.

• Polymerases and Ligases:

  • Enzymes that join molecules together, crucial in processes such as DNA replication.

• Lyases and Hydrolases:

  • Lyases break down molecules, while hydrolases perform hydrolysis, using water to split compounds.

Enzyme Structure & Functionality

• Enzymes can be composed of proteins alone or proteins plus additional components (cofactors or coenzymes).

• Holoenzyme: Active form of an enzyme that binds to its substrate and is capable of catalyzing a reaction.

• Apoenzyme: Inactive form of an enzyme that requires an additional component (cofactor/coenzyme) to be functional.

Binding and Interaction Models

• Induced Fit Model:

  • The model describes how a substrate induces a change in the enzyme's active site to fit perfectly upon binding.

• Enzyme-Substrate Complex: The temporary complex formed when an enzyme binds its substrate.

Impact of Environmental Conditions on Enzyme Activity

• Temperature:

  • Enzymes have an optimal temperature for activity, typically around 37°C for human enzymes.

  • High or low temperatures can lead to denaturing, where enzymes lose their functional shape and cease to work.

• pH:

  • Each enzyme functions optimally at a specific pH.

  • Changes in pH can affect the hydrogen bonds within proteins, altering their structure and activity.

Enzyme Concentration and Substrate Availability

• As enzyme concentration increases, the rate of reaction generally increases, given an ample supply of substrates.

• Saturation Point: The maximum rate of reaction, determined by the available number of enzymes.

Inhibition Mechanisms in Enzyme Function

• Competitive Inhibition:

  • Occurs when an inhibitor binds to the active site, preventing substrate binding.

• Non-competitive Inhibition:

  • Inhibitor binds to an allosteric site, causing a change in the enzyme shape that prevents substrate binding at the active site.

• Feedback Inhibition:

  • A product of a metabolic pathway inhibits an early enzyme in that pathway to prevent overproduction when sufficient product accumulates.

Overview of Redox Reactions

• Redox Reactions:

  • These reactions involve the transfer of electrons between reactants, comprising both oxidation (loss of electrons) and reduction (gain of electrons).

  • The relation can be remembered with the acronym "LEO says GER" (Lose Electrons: Oxidized; Gain Electrons: Reduced).

Electron Carriers and ATP Production

• Electron Carriers: Modified nucleotides such as NAD, NADP, and FAD, are crucial for transferring electrons during metabolic processes.

• ATP (Adenosine Triphosphate):

  • ATP is a nucleotide composed of adenine and three phosphates, serving as the primary energy currency in cells.

  • Phosphorylation: Process of adding a phosphate group to ADP to form ATP, which can occur via substrate-level phosphorylation or through electron transport chains during oxidative or photophosphorylation.