Biological Reactions and Enzymatic Activity

Cellular Energy and Enzymes

Understanding Energy

  • Energy:

    • Definition: The ability to do work, which involves any change in the state or motion of matter.

    • All living systems require energy to survive and function.

    • To sustain life, energy input must exceed energy output.

    • Any loss of order or energy flow can result in death.

Energy Input in Cells

  • Cells implement metabolic pathways to extract energy from different sources and can be identified as conserved across all life domains, supporting the common ancestry of life.

  • Cells receive energy in various forms (e.g., light, organic molecules like glucose) which must be converted before utilization.

    • Types: kinetic energy and potential (chemical) energy.

Laws of Thermodynamics

  • The study of energy transformations in matter is termed thermodynamics, with two principal laws applicable to universal mechanics.

First Law of Thermodynamics

  • Energy cannot be created nor destroyed but can be transformed or transferred.

  • Example: The chemical (potential) energy stored in food (e.g., nuts) transforms into kinetic energy for animals (e.g., a squirrel climbing a tree).

Second Law of Thermodynamics

  • Energy transformation increases entropy, which is a measure of disorder.

    • Energy conversions often release heat, signifying less usable energy (disorganization) for performing other useful work.

  • Example: As a squirrel climbs, it releases some energy as heat.

Misconceptions About Entropy

  • Cellular organization doesn’t violate the second law of thermodynamics because while the entropy of organisms may decrease, the total entropy of the universe increases.

Metabolism

  • Metabolism: The sum of all chemical reactions in a cell that transform energy and matter, which includes metabolic pathways that can be categorized as catabolic (breakdown) or anabolic (building up).

    • Metabolic pathways are structured sequentially, where the product of one reaction serves as a reactant in the next.

    • Diagram: Substrate → Intermediate → Product with respective enzymes acting in the pathway.

Catabolism vs. Anabolism

  • Catabolism: The process breaking down complex molecules into smaller units to release energy.

  • Anabolism: The process building complex molecules from simpler ones, requiring energy.

Energy in Reactions

  • Reactions can be classified as either endergonic (requiring energy) or exergonic (releasing energy).

    • Reactions requiring energy often couple with those releasing energy, typically mediated through ATP.

    • Definitions:

    • Endo = within; Ex = out; Ergon = work (Greek).

Adenosine Triphosphate (ATP)

  • ATP: Molecule utilized by organisms as a source of energy to perform work, structured with adenine, ribose, and three phosphate groups.

Coupling Reactions via ATP

  • Energy-requiring reactions within cells occur through coupling them with ATP hydrolysis.

    • Reaction: ATP + H₂O → ADP + Pi where released phosphate phosphorylates other molecules, enhancing reactivity.

Regeneration of ATP

  • ATP is regenerated from ADP through the ATP cycle, where energy for synthesis comes from other exergonic reactions in the cell (e.g., cellular respiration).

Energy Requirements in Cells

  • Cells require energy for various processes, including:

    • A: Movement

    • B: Pumping substances across membranes

    • C: Protein synthesis

Rate of Metabolic Reactions

  • While thermodynamic laws predict reaction occurrence, they do not predict the rates. Some reactions (e.g., sucrose hydrolysis) are exceedingly slow.

  • Enzymes, biological catalysts, accelerate reaction rates by lowering activation energy, which is the initial energy input required to commence a reaction.

Function of Enzymes

  • Enzymes: Proteins that catalyze reactions by:

    • Bringing reacting molecules close together correctly

    • Altering the substrate shape via charged active sites to encourage catalysis.

Enzyme-Substrate Complex

  • Upon substrate binding, enzymes and substrates slightly change shape, forming an enzyme-substrate complex to facilitate bond changes in reaction products.

Structure and Function of Enzymes

  • Active Site: The specific area on the enzyme where the substrate binds, emphasizing that enzymes act on compatible substrates.

Enzyme Cofactors

  • Enzymes may require cofactors:

    • Cofactors: Non-protein molecules assisting enzyme functions, e.g., metallic ions or organic coenzymes like NAD+.

    • Effects on catalysis: assist in reactions and serve as electron carriers.

Differences between Cofactors and Coenzymes

  • Cofactors can be:

    • Inorganic (metal ions) or organic, while coenzymes are always organic.

    • Cofactors are often tightly bound, assisting enzymes in their active states.

Implications of Enzyme Activity

  • Biochemical processes emphasize the pivotal role of enzymes in digestion (e.g., ptyalin and pepsin) without which complex foods cannot be efficiently processed.

Experiment Evaluation

  1. Data examination of ptyalin and pepsin activity under varying pH levels.

  2. Optimal pH identification for both enzymes based on experimental evidence.

  3. Links between optimal pH and enzyme locations in the body.

  4. Consequences of pH deviation from optimal conditions in enzyme functionality.

Factors Affecting Enzyme Activity

Shape Changes

  • Structural conformation changes (denaturation) affect enzyme efficiency due to perturbations in the 3D shape held by diverse interactions/bonds.

Denaturation Details

  • Denaturation: Loss of enzyme structure and function due to environmental conditions. Sometimes reversible if the primary structure is intact.

Conditions Leading to Denaturation

  • Effects of Temperature: Beyond optimal temperature, heat can disrupt bonds stabilizing protein conformation.

  • Effects of pH: Alters hydrogen bonds and changes amino acid charges, leading to modified active sites.

  • Chemical Environment: External substances (salts, solvents) can unfold proteins, causing loss of function.

Substrate Concentration Effects

  • Enzyme reaction rates depend on substrate concentration:

    • Low substrates: Infrequent collisions with enzymes lead to slow reactions.

    • High substrates increase rates until enzymes reach saturation.

Regulation of Enzyme Activity

  • Cell activity adjusts via:

    • Competitive and non-competitive inhibition

    • Allosteric regulation.

Competitive Inhibition

  • Competitive inhibitors block substrates from binding the active site while some inhibitor effects are reversible through increased substrate concentrations.

Non-Competitive Inhibition

  • Non-competitive inhibitors bind elsewhere on the enzyme (allosteric site), altering the active site shape and preventing substrate binding.

    • Types of inhibition may be permanent (covalent binding) or reversible (weak interactions).

Allosteric Regulation

  • Involves molecules binding to allosteric sites affecting enzyme activity, either enhancing (activators) or diminishing (inhibitors) function.

    • Unique enzymes may possess multiple active sites with allosteric control.

Feedback Inhibition

  • This mechanism occurs when the end product in a metabolic pathway serves as an allosteric inhibitor for an early enzyme, regulating the pathway's overall activity.