Proteins and Enzymes Flashcards

Energy and Enzymes

Introduction

• This lecture focuses on enzymes, a crucial class of proteins for sustaining life.
• It covers energy transformations in cells, enzyme functions, and basic enzyme regulation.

Energy Transformations

• Energy transformation is essential for life.
• Energy is defined as the capacity to do work or cause change.
• Biological energy transformations involve chemical reactions where energy is transferred between molecules.
• It's the process of chemicals changing; it's the action of detaching a lump of chemical to attach to another.

Forms of Energy

• Potential Energy
  • Stored energy, such as in food molecules like glucose.
  • Glucose contains high-energy electrons that can be accessed to extract energy.
• Kinetic Energy
  • Energy of motion.
  • Regulated by metabolic processes.

Metabolism

• Metabolism is the set of chemical reactions that enable organisms to live, grow, reproduce, etc.
• Anabolic Reactions
  • Synthesis of complex molecules from simpler ones (e.g., DNA from nucleotides, proteins from amino acids).
  • Require energy input.
• Catabolic Reactions
  • Breakdown of complex molecules to release energy (e.g., extracting energy from food molecules).

Thermodynamics

• The laws of thermodynamics explain how cells extract energy.

First Law of Thermodynamics

• Energy is neither created nor destroyed; it is converted from one form to another.
• The total energy before and after conversion remains the same.

Second Law of Thermodynamics

• Energy conversions are not 100% efficient; some energy is lost as unusable energy (e.g., heat).

Entropy

• Entropy is the measure of disorder in a system.
• Living organisms require energy to maintain ordered structures.
• When an organism dies, it breaks down due to increased disorder.

Energy and Disorder

• Over time, unusable energy accumulates, leading to increased disorder.
• Total energy in a system includes usable (free) energy and unusable energy.
• Formula:
  • H = G + TS
  • Where:
    • H is enthalpy (heat of all molecules).
    • G is free energy.
    • T is temperature.
    • S is entropy.
• Rearrangement:
  • \Delta G = \Delta H - T\Delta S

Free Energy

• Free energy (\Delta G) is the energy available to do work in a reaction.
• Measured in calories or joules.
• The change in free energy (\Delta G) is the difference between the energy of the initial and final molecules.
• If \Delta G is negative, free energy is released (exergonic reaction).
• If \Delta G is positive, free energy is required (endergonic reaction).
• If \Delta G is zero, the reaction is at equilibrium or the organism is dead.
• Gibbs Free Energy named after Josiah Willard Gibbs
• Formula:
  • \Delta G = G{\text{products}} - G{\text{reactants}}

Hydrolysis of Protein Example

• Hydrolysis (breaking a covalent bond by adding water) of a protein increases entropy because it creates more disorder.

Order vs. Disorder in Biological Systems

• Life requires highly ordered structures at all levels (e.g., fly eye, microorganisms, cellular level).
• Living organisms must counteract the tendency to increase disorder by supplying energy.

Exergonic and Endergonic Reactions

• Exergonic Reactions
  • Release free energy (catabolism).
  • Decrease complexity.
  • Reactants have more free energy than products.
  • Analogy: Ball rolling down a hill.
• Endergonic Reactions
  • Consume free energy.
  • Increase complexity/order.
  • Products have more free energy than reactants.
  • Analogy: Ball rolling uphill (requires a push).

Reversible Reactions

• Chemical reactions can proceed in both directions (forward and reverse).
• Equilibrium is reached when the forward and reverse reactions balance.
• The \Delta G value is related to the equilibrium point.
• In biochemical pathways, products are immediately used in subsequent reactions, preventing equilibrium.
• A \Delta G value close to zero indicates that the reaction can work in both directions without requiring much energy input or release.
• Example: Glucose-6-phosphate has different equilibrium points in a lab vs. in a cell, due to immediate consumption of products in the cell.

Enzymes: Biological Catalysts

Definition

• Enzymes are biological catalysts that speed up reactions without being altered themselves.
• Most enzymes are proteins (some are RNA (ribozymes)).
• They act as a framework for reactions to occur.
• Reactions often do not occur quickly or at all without enzymes due to energy barriers.

Activation Energy

• Activation energy is the energy required to start a reaction.
• Enzymes lower the activation energy.
• Reactions proceed through an unstable intermediate state.
• It takes energy to contort, twist, or bring molecules together for a chemical restructuring.

Enzymes Lowering Activation Energy

• Enzymes lower activation energy by bringing reactants together.
  • Every reaction in cells is catalyzed by a specific enzyme.
  • There are thousands of genes encoding enzymes.

Substrates and Active Sites

• Substrate: the material that undergoes a reaction that is catalyzed by an enzyme.
• Enzymes are highly specific to their substrates.
• The active site (binding pocket) is the region of the enzyme where the substrate binds.
• The active site's shape is specific to the substrate molecule(s).
• The active site contains amino acids with specific R groups that interact with the substrate (ionic, polar, hydrogen bonds).
• Diagram:
  • Enzyme + Substrate –> Enzyme-Substrate Complex –> Enzyme + Product
• Enzymes are beneficial because they lower the reaction's energy barrier.

Mechanisms of Enzyme Action

• Enzymes lower activation energy through various mechanisms:

Orientation

• Enzymes orient substrate molecules to facilitate the reaction.
• Ensuring the perfect atom alignment
• Example: Citrate synthase brings two substrate molecules into close proximity.

Physical Strain

• Enzymes strain or distort the substrate molecule.
• Enzymes contort the structure.
• Example: Lysozyme, found in tears, breaks down bacterial cell walls by straining protein structure.

Chemical Charge

• Enzymes chemically modify the substrate.
• Making molecules become ionic.
• Example: Chymotrypsin cuts up proteins using ionic amino acids in the binding site.
• Form and function are interlinked in enzyme activity.

Lock and Key vs. Induced Fit

• Enzymes do NOT work via a lock-and-key mechanism, where they match their substrate perfectly because then there would be no reaction whatsoever as the structure would stabilize.
• Lock and key is rubbish because matched active site would stabilize the structure.
• Induced fit model: enzymes change shape upon substrate binding.
• Active sites force the reaction to happen.
• Enzymes destabilize structures, which is the opposite of the stabilizing process from a lock and key model.

Enzyme Regulation and Metabolic Pathways

Overview

• Metabolic pathways organize reactions; the product of one reaction becomes the substrate for the next.
• These metabolic pathways are heavily interconnected and must be regulated.
• They interconnect like a tube map.
• The needs of the cell open some sets of processes one way and shut others down.
• Enzymes are regulated based on their importance in these interactions and heavily ordered pathways.
• The first reaction is where the important part of the regulation happens.
• Feedback inhibition is crucial in regulation.

Feedback Inhibition

• The end product of a pathway inhibits the first enzyme in the pathway.
  • Example: In amino acid production, threonine is converted to isoleucine.
  • Isoleucine binds to the first enzyme, inhibiting its activity and is regulated physically by the isoleucine amino acid.
  • Nitrogen difficult to obtain biologically, so kept one obtained.
  • When isoleucine levels drop, the pathway restarts.

Other Factors Affecting Enzyme Function

• pH
  • Digestive enzymes work at specific pH levels.
  • High and low pHs impact protein folding and activity.
  • Example: Pepsin in the stomach works best at pH 2 and stops at other pH levels.
• Temperature
  • Enzymes function best within optimal temperature ranges.
  • Outside this range, they lose their structure and stop working.

Ribozymes: RNA Enzymes

• Ribozymes are enzyme-like molecules made from RNA.
• They act as biological catalysts and cut RNA transcripts.
• RNA may have existed and catalyzed reactions before proteins came along.