Lecture 2_BIOL7001

Page 1: Course Introduction

  • Institution: MTU Ollscoil Teicneolaíochta na Mumhan (Munster Technological University)

  • Course Code: BIOL7001

  • Topic: Applied Enzymology - Lecture 2

  • Instructor: Fiona O'Halloran (Contact: Fiona.ohalloran@mtu.ie)

  • Date: September 2024

Page 2: Activation Energy

  • Definition: The energy barrier preventing spontaneous reactions.

  • Impact on Reaction Rate:

    • Higher activation energy (Ea) results in a slower reaction rate.

Page 3: Role of Biological Catalysts

  • Function:

    • Lower the free energy of activation (ΔG‡/Ea) without affecting the equilibrium of the reaction.

  • Effect:

    • Enhance the rates of both forward and reverse reactions equally, favoring thermodynamically favorable reactions.

Page 4: Increasing Reaction Rates

  • Question Explored: What mechanisms can increase the rate of a chemical reaction?

  • Consideration for Biological Systems: Are these mechanisms applicable in biological systems?

Page 5: Enzyme Mechanism Description

  • Catalytic Action of Enzymes:

    • Without Enzyme:

      • AG+ leads to the formation of Transition State, then Products.

    • With Enzyme:

      • Enzyme is complementary to the substrate, facilitating transition states.

    • Visual Representation: Describes the relationship between substrate (S), enzyme (E), and products (P) in terms of activation energies and reaction coordinates.

Page 6: Enzyme Characteristics

  • Efficiency:

    • Example: Orotidine 5’-phosphate decarboxylase catalyzes reactions at a rate of 1 x 10^17 / second.

    • Function: Decarboxylates orotidine monophosphate (OMP) to uridine monophosphate (UMP) in pyrimidine biosynthesis.

Page 7: Specificity of Enzymes

  • Highly Specific Catalysts:

    • Example 1: Proteases

      • Trypsin: Cleaves at C-terminal side of positively charged amino acids.

      • Pepsin: Prefers cleavage at N-terminal of aromatic amino acids.

    • Example 2: Isoenzymes

      • Glucokinase is an isoform of hexokinase with specific D-glucose reactivity.

      • Different kinetics may have significant biological implications for metabolic pathways.

Page 8: Important Features and Terms

  • Enzymes: Mostly proteins containing active sites.

  • Cofactors/Coezymes: Enhance enzyme functionality.

  • Types:

    • Holoenzyme: Active enzyme with cofactor.

    • Apoenzyme: Inactive form of the enzyme without a cofactor.

  • Types of Cofactors:

    • Low molecular weight organic molecules (e.g., NAD(P)H).

    • Metal ions (e.g., Cu++, Zn++, Fe++, Co++).

Page 9: IUB Classification of Enzymes

  • Enzyme Categories:

    • Oxidoreductase (EC1): Transfer of electrons (e.g., Lipoxidases, Dehydrogenases).

    • Transferase (EC2): Transfer of groups between molecules (e.g., Aminotransferase, Lactase).

    • Hydrolase (EC3): Cleavage via water (e.g., Proteases, Trypsin).

    • Lyase (EC4): Addition or removal of groups to/from double bonds.

    • Isomerase (EC5): Transfer of groups within a molecule (e.g., Topoisomerase, Glucose isomerase).

    • Ligase (EC6): Joining of two molecules (e.g., Aminoacyl tRNA synthetase).

    • Translocases (EC7): Movement of ions/molecules across membranes (e.g., ATP synthase).

Page 10: Enzyme-Substrate Binding Theories

  • Accepted Theories:

    • A. Emil Fischer - Lock and Key Theory.

    • B. Daniel Koshland - Induced Fit Theory.

Page 11: ES Complex Formation

  • Formation: Rapid and reversible binding of enzymes to substrates.

  • Reaction Sequence:

    • E + S ⇌ ES → E + P

  • Reaction Rate Dynamics:

    • Hyperbolic relationship observed between the rate of reaction and substrate concentration [S].

    • At constant enzyme concentration [E], reaction rate rises with substrate concentration until maximum velocity is achieved.

Page 12: Enzyme Concentration Control

  • Rate Relationship:

    • Unlike substrate concentration scenarios, reaction rate is proportional to enzyme concentration when substrate is non-limiting.

  • Biological Control Mechanisms:

    • Inquiry into what factors regulate enzyme concentrations in biological systems.


The tree diagram on page 8 illustrates important features and classifications of enzymes, particularly dealing with enzymes, cofactors, and their forms:

  • Enzymes: Primarily proteins that contain active sites essential for their function.

  • Cofactors/Coezymes: These are substances that enhance the functionality of enzymes and can be classified as:

    • Holoenzyme: The active form of an enzyme that includes its necessary cofactor.

    • Apoenzyme: The inactive form of the enzyme that lacks its cofactor.

  • Types of Cofactors: They can be further divided into:

    • Low molecular weight organic molecules (e.g., NAD(P)H).

    • Metal ions (e.g., Cu++, Zn++, Fe++, Co++).

This classification helps in understanding how different components interact to facilitate enzymatic reactions in biological systems.