Notes

• Role of enzymes in metabolism


  Metabolism describes the totality of all enzyme-catalysed reactions that occur within a living cell or organism

  • Because of enzyme specificity, many different enzymes are required by living organisms, and control over metabolism can be exerted through these enzymes.

  Metabolic reactions serve two key functions:

  • They provide a source of energy for cellular processes (growth, reproduction, etc.)
  • They enable the synthesis and assimilation of new materials for use within the cell
• Anabolic Reactions


  • Anabolic reactions describe the set of metabolic reactions that build up complex molecules from simpler ones
  • The synthesis of organic molecules via anabolism occurs via condensation reactions (water is produced)
  • Examples of anabolic reactions include:
  • The production of glucose by photosynthesis (and its subsequent polymerisation into glycogen / starch)
  • The synthesis of polypeptide chains (proteins) from amino acid subunits (i.e. translation at the ribosomes)
  • The semi-conservative replication of DNA and the formation of RNA transcripts via transcription

  
• Catabolic Reactions


  • Catabolic reactions describe the set of metabolic reactions that break down complex molecules into simpler ones
  • The breakdown of organic molecules via catabolism occurs via hydrolysis reactions (water is consumed)
  • Examples of catabolic reactions include:
  • The oxidation of substrates in cell respiration (i.e. breaking down glucose via glycolysis or the Krebs cycle)
  • The breakdown of macromolecules (polymers) into monomers during the process of chemical digestion

  
• Active site



  • Region on the surface of the enzyme to which a substrate molecule binds. Composed of a few amino acids.
  • Interactions between these amino acids ensure the overall shape and chemical properties complement the substrate

  
• Activation energy (EA)


  The amount of energy required for a chemical reaction to proceed. Speed up the rate of a biochemical reaction.

  Lower the activation energy, meaning less energy is needed to convert the substrate into a product.

  The reaction proceeds at a faster rate.
• Enzymes


  An enzyme is a globular protein which acts as a biological catalyst by speeding up the rate of a chemical reaction

  • Enzymes are not changed or consumed by the reactions they catalyse and can be reused (hence are only required in low amounts)

  Enzymes are typically named after the molecules they react with (called the substrate) and end with the suffix ‘-ase’

  • For example, lipids are broken down by the enzyme lipase while proteins are digested by proteases
• Reactions 


  Catabolic reactions involve the breaking down of molecules, resulting in the release of energy from the broken bonds. When the reactants have more energy than the products, the excess energy is released into the system. These reactions are referred to as exergonic reactions.

  Anabolic reactions involve the process of building up, requiring energy to synthesize bonds between molecules. In these reactions, if the reactants have less energy than the products, the excess energy is absorbed from the system. These reactions are known as endergonic reactions.

  
• Catalyst


  A catalyst is a substance that allows a reaction to proceed at a faster rate or underconditions otherwise different possible

  • Enzymes are biological catalysts that are not consumed by the specific reactions they catalyse (so can operate in low amounts)
• Enzymes as Catalyst

  Enzymes allow chemical reactions to proceed within a biologically relevant passage of time

  • Without enzymes, DNA replication would be unable to occur within the lifetime of a cell (preventing organismal growth and repair)
  • Without enzymes, food would be unable to be chemically digested within the period of transit through the digestive tract (meaning insufficient nutrient absorption)
• Enzymes and Temperature Regulation in Chemical Reactions


  Enzymes also allow for chemical reactions to proceed at biologically appropriate temperatures

  • Without enzymes, chemical reactions would require higher temperatures which could denature cell components (homeostasis would not be maintained)
• Enzyme Catalysis and Substrate Interaction


  Enzyme catalysis requires that the substrate be brought into close physical proximity with the active site

  • When a substrate binds to the enzyme’s active site, an enzyme-substrate complex is formed
  • The enzyme catalyses the conversion of the substrate into product, creating an enzyme-product complex
  • The enzyme and product then dissociate – as the enzyme was not consumed, it can continue to catalyse further reactions
• The induced fit model


  According to the induced fit model, the enzyme’s active site is not a completely rigid fit for the substrate

  • Instead, the active site will undergo a conformational change when exposed to a substrate to improve binding
  • This explains how enzymes may exhibit broad specificity (e.g. lipase can bind to a variety of lipids)
  • It also explains how catalysis may occur (the conformational change stresses bonds in the substrate, increasing reactivity)

  
• Role of molecular motion and substrate-active site collisions in enzyme catalysis


  1. Enzyme reactions occur in aqueous solutions (cytoplasm, interstitial fluid)

  2. Substrate and enzyme move randomly (Brownian motion)

  3. Enzyme may be fixed in position (e.g. membrane-bound) to localise reactions to particular sites

  4. Substrate and enzyme must physically collide in the correct orientation to facilitate binding to the active site
• Increasing the rate of enzyme catalysis


  1. Increasing the frequency of collisions

  2. Increasing the molecular motion of the particles (thermal energy can be introduced to increase kinetic energy)

  3. Increasing the concentration of particles (either substrate or enzyme concentrations)
• Active site


  Indentation or cavity to which the substrate can bind with high specificity. Shape and chemical properties are highly dependent on the three dimensional shape of the enzyme.
• Enzyme structure


  Can be modified by external factors such as high temperatures and extreme pH. Disruption of the chemical bonds which are necessary to maintain the shape and chemical properties of the enzyme. Negatively affects the enzyme's capacity to bind the substrate.
• Inhibitors


  Molecules that may reduce enzyme-substrate interactions by either occluding the active site or altering its shape

  
• Factors affecting the rate of enzyme activities 


  Various factors may affect the activity of enzymes, by either affecting the frequency of enzyme-substrate collisions or by affecting the capacity for the enzyme and substrate to interact (e.g. denaturation)

  • Temperature, pH and substrate concentration will all influence the rate of activity of an enzyme
• Effects of pH on the rate of enzyme activity


  • Changing the pH will alter the charge of the enzyme, which in turn will alter protein solubility and overall shape
  • Changing the shape or charge of the active site will diminish its ability to bind the substrate, abrogating enzyme function
  • Enzymes have an optimal pH (may differ between enzymes) and moving outside this range diminishes enzyme activity

  
• Effects of temperature on the rate of enzyme activity

  • Low temperatures lack sufficient energy for enzyme-catalyzed reactions and the enzyme molecules have less kinetic energy or fewer successful collisions, which decreases the rate of the reaction
  • Increased temperature boosts enzyme and substrate motion, leading to higher activity.
  • Optimal temperature (varies by enzyme) maximizes enzyme activity.
  • Higher temperatures disrupt enzyme stability, causing denaturation and loss of activity

  
• Effects of Substrate Concentration on the rate of enzyme activity

  • Increasing substrate concentration will increase the activity of a corresponding enzyme
  • More substrates mean there is an increased chance of enzyme and substrate colliding and reacting within a given period
  • After a certain point, the rate of activity will cease to rise regardless of any further increases in substrate levels
  • This is because the environment is saturated with substrate and all enzymes are bound and reacting (Vmax)

  
• Measurements in enzyme-catalysed reactions


  • Which specific enzyme / substrate reaction to investigate
  • Which experimental factor to manipulate (i.e. the independent variable)
  • How to measure the enzyme activity (i.e. the dependent variable)
• Calculating and plotting the rate of an enzyme-catalysed reaction


  1. Measure the time taken for the reaction to proceed

  2. According to the amount of product formed

  3. According to the amount of substrate consumed
• Reaction rate


  The inverse of time taken, meaning that the reaction rate is higher when less time is taken (and vice versa)
• Enzyme–substrate specificity


  Enzymes are proteins with specific 3-D geometry/shape. Enzymes with active site that binds with the substrate/reactants

  Active site shape only allows it to bind with specific substrates «with complementary shapes»

  When enzyme-substrate complex formed allows reaction to occur

  Products are released and enzyme returns to original shape and can be reused