Enzymes: Structure, Function, Kinetics, and Regulation - Lecture Notes

Enzymes as Biological Catalysts

  • Enzymes are biological catalysts. They speed up chemical reactions and are not consumed in the process.
  • The idea of a catalyst lasting for the life of your car (e.g., catalytic converter) is used as an analogy: it facilitates the reaction, produces byproducts, and is not used up.
  • Not all catalysts are proteins; some catalysts are not enzymes per se.
  • Enzymes are biological catalysts that help reactions occur by lowering activation energy, not by changing the overall energy of the reactants or products.

Enzyme Structure and the Active Site

  • An enzyme is a protein with a specific 3D structure that includes an active site where substrates interact.
  • Lock-and-key is an outdated simplification; enzymes are not rigid doors that only fit one lock. They change shape and are flexible (induced fit).
  • The goal of the enzyme is to bring substrates into close proximity so they can overcome repulsive forces (e.g., electron repulsion) and react to form products.
  • Substrates enter the active site and interact there to form products; the enzyme is not consumed and can catalyze additional reactions.
  • Enzymes are not fixed in shape; there is flexibility that allows interaction with the substrate
    • This flexibility is important for specificity to a particular substrate.
  • Coenzymes and cofactors can bind to the enzyme to help the reaction:
    • A coenzyme is an organic molecule (e.g., a vitamin derivative).
    • A cofactor can be an inorganic ion or a molecule; some cofactors are bound at the active site to assist catalysis.
    • Example: NAD^+ as a major electron carrier (a coenzyme).
  • The enzyme–cofactor system is described as apoenzyme vs holoenzyme:
    • Apoenzyme: the enzyme alone, without the cofactor.
    • Holoenzyme: the enzyme with the cofactor bound, i.e., the complete active enzyme.
  • In some cases, the coenzyme binds at the active site and directly facilitates the substrate interaction.

Enzyme Naming, Substrates, and Specificity

  • Enzymes have prefixes and suffixes that hint at their function:
    • Ligases: to bind together (e.g., form a bond between molecules).
    • Lyases: to cleave or split apart (e.g., break bonds).
    • Dehydrogenases (e.g., pyruvate dehydrogenase): indicate the substrate (pyruvate) and the action (dehydrogenation, removal of hydrogen).
    • Lactases: act on lactose (substrate is lactose).
    • DNA ligase: links DNA strands together to form a polymer.
  • The takeaway is to recognize the class and the general description, not memorize a full table of every enzyme.
  • An example to illustrate naming:
    • Pyruvate dehydrogenase – acts on pyruvate and involves removal of hydrogen (dehydrogenase).
    • Lactase – acts on lactose.
    • DNA ligase – links DNA strands.

Enzyme Substrate Interactions and Saturation

  • Substrate concentration and enzyme concentration determine how fast the reaction proceeds:
    • One enzyme molecule can process two substrate molecules to form a product in a single turnover, so a single enzyme can handle a limited number of substrates at a time.
    • If you have many enzyme molecules and fewer substrate molecules, each enzyme processes one substrate at a time and then is available for another.
    • If substrate concentration greatly exceeds enzyme concentration, the reaction becomes saturated: the enzyme active sites are occupied and adding more substrate does not increase the rate.
  • Conceptual relationships:
    • With, for example, 10 enzyme molecules, you could process up to 10 substrates concurrently (assuming each enzyme acts on a substrate at a time).
    • If substrate concentration remains high while enzyme concentration is fixed, you reach saturation and the rate is limited by the number of active sites.
  • This dependence of rate on enzyme and substrate concentrations is foundational for understanding enzyme kinetics.
  • A common way to think about what happens at the active site is: bring substrates together so they can react, and the enzyme is reused after product formation.

Temperature and pH Effects on Enzyme Activity

  • Temperature:
    • As temperature rises, enzyme activity generally increases due to increased molecular motion (Brownian motion).
    • Beyond an optimum temperature, proteins begin to denature, losing their proper folding and active shape (
      denaturation).
    • Denaturation can be irreversible for some proteins (e.g., eggs being fried): the protein unfolds and cannot return to its original functional shape.
  • pH:
    • Enzymes have an optimal pH (often a narrow range). Moving away from this range can disrupt hydrogen bonding and the overall shape, leading to denaturation.
    • Very acidic or very basic conditions can disrupt the enzyme’s structure and activity.
    • In stomach, proteolytic enzymes operate in highly acidic conditions (low pH), which helps protein breakdown.
  • Renaturation:
    • In some cases, proteins can regain their proper fold if conditions return to favorable states; however, this is not universal for all proteins or under all circumstances.
  • Visualization:
    • An egg white analogy can illustrate progressive denaturation: heat starts at the edges and progresses inward, showing that denaturation often occurs gradually and can be partially reversible depending on the protein and conditions.

Inhibitors: Competitive and Noncompetitive

  • Enzyme activity can be inhibited by other molecules called inhibitors.
  • Competitive inhibitors:
    • Bind to the active site of the enzyme, competing with the substrate for access to the active site.
    • If the substrate concentration increases, it can outcompete the inhibitor, freeing the active site for substrate binding.
    • This inhibition is concentration-dependent: more substrate can displace the inhibitor from the active site.
    • Conceptually, competition occurs at the same site (the active site) where substrate binding occurs.
  • Noncompetitive inhibitors:
    • Bind to an enzyme at a site other than the active site (an allosteric site).
    • Binding causes a conformational change in the enzyme, reducing or abolishing its ability to bind substrate effectively, even if substrate concentration is high.
    • Increasing substrate concentration cannot outcompete a noncompetitive inhibitor because the inhibitor affects the enzyme regardless of substrate presence.
  • The presence of inhibitors can dramatically affect the rate of reaction by altering how many active enzymes are available or how effectively the active site can interact with substrate.

Practical Takeaways and Connections

  • Enzymes are flexible proteins (not rigid) that catalyze reactions by bringing substrates together in the active site and often with the help of cofactors or coenzymes like NAD^+.
  • The enzyme’s activity depends on substrate and enzyme concentrations, temperature, pH, and potential inhibitors.
  • Enzymes can be regulated by various factors, including inhibitors, cofactors, and the local environment (temperature and pH).
  • The concept of apoenzyme vs holoenzyme is important for understanding when an enzyme is active and how cofactors influence activity.
  • Metabolic pathways (to be discussed next) involve sequences of enzyme-catalyzed steps, with regulation ensuring that the flow of metabolites is coordinated and efficient.

Quick Reference: Key Terms from the Transcript

  • Apoenzyme: enzyme without its cofactor.
  • Holoenzyme: enzyme with its cofactor bound.
  • Coenzyme: organic non-protein helper (e.g.,
    extNAD+ext{NAD}^+).
  • Cofactor: inorganic or organic molecule that aids enzyme function.
  • Active site: region of the enzyme where substrate binding and catalysis occur; not a fixed lock-and-key site, but a flexible region.
  • Substrate: molecule that binds to the enzyme and is transformed into product.
  • Inhibitor: molecule that reduces enzyme activity; can be competitive or noncompetitive.
  • Competitive inhibitor: binds at the active site, can be displaced by substrate.
  • Noncompetitive inhibitor: binds at a site other than the active site, causes conformational change, cannot be displaced by substrate.
  • Saturation: condition where all enzyme active sites are occupied, limiting the rate regardless of substrate excess.
  • Denaturation: loss of protein structure due to extreme conditions (temperature/pH), often irreversible in severe cases.
  • Renaturation: partial or full return to functional structure under favorable conditions (protein-dependent).
  • Induced fit: the enzyme changes shape upon substrate binding to facilitate catalysis (more accurate than rigid lock-and-key).
  • Pyruvate dehydrogenase, lactase, DNA ligase: examples of enzyme classes and substrates, illustrating naming patterns.
  • NAD^+: a common coenzyme involved in electron transfer and oxidation-reduction reactions.
  • Metabolic pathways: planned to be discussed next; involve enzymes in sequences with regulatory control.