Lecture 3: Enzymes and biochemical pathways

Enzymes & Biochemical Pathways

• Enzymes are biological catalysts that facilitate metabolic reactions, but do not add energy. They only speed up the rate of reactions.
• Catabolic pathways break down molecules to release energy and produce intermediate metabolites.
• Anabolic pathways use energy to build up molecules.
• Metabolism refers to all chemical reactions within an organism.

Metabolism & Cellular Environment

• Metabolic pathways are either catabolic or anabolic.
• Enzymes are biological catalysts, facilitating metabolic reactions, but not adding energy to the reactions.
• They increase the speed of reactions.
• Enzymes only use the activation energy for reactions and then are reusable.

How Cells Use Energy

• Biological systems obey the laws of thermodynamics.
• Conservation of energy: energy cannot be created or destroyed. Energy must be put into a system for work to occur.
• Entropy (disorder) tends to increase over time; energy flows down a gradient (high to low).
• Energy is always required to create organization or to decrease entropy.
• Examples include organized metabolic pathways, cytoskeleton structure, organelles, DNA sequences, and active transport.
• Heat energy is always present.

Types of Energy

• Energy is the capacity to cause change (to do work).
• Energy exists in various forms, falling into two categories:
  • Kinetic energy—energy associated with motion, including heat energy due to random molecular motion.
  • Potential energy—energy that matter possesses due to its structure or location.
    • Chemical energy—potential energy stored in chemical bonds that can be released in chemical reactions.
  • Molecules or ions concentrated on one side of a membrane can represent potential energy.

How Cells Use Energy (Conversion of Energy)

• Not all forms of energy are useful to a cell
• Cells convert energy from one form to another.
• Examples include: the energy stored in the bonds of a sugar molecule, which cannot pump ions across a membrane but can be broken and transformed to make ATP
• This ATP can be used by an active transport pump that moves ions
• Small molecule waste products such as CO2 and H2O carry away energy as heat.

Photosynthesis

• Cells that can carry out photosynthesis use the energy of sunlight to drive biochemical reactions that transform electromagnetic energy into chemical energy (covalent bonds).

Redox Reactions

• Oxidation and reduction reactions (redox reactions) involve electron transfer; these reactions are used to ferry energy between reactions
• Photosynthesis and cell respiration involve redox reactions

Free Energy and Catalysis

• In complex reactions, the equilibrium constant (K) includes the concentrations of all reactants and products. K will tell you the concentrations when equilibrium is reached.
• The change in free energy (ΔG) is related to the equilibrium constant.
• For sequential reactions, free energy changes are additive.
• The change of Gibb's free energy is written as ΔG and tells how much energy is needed for a reaction to occur
• Reactions that occur spontaneously have a negative ΔG whereas reactions that are not spontaneous have a positive ΔG.
• Enzyme-catalyzed reactions depend on rapid molecular collisions.

Enzymes

• Enzymes are biological catalysts made of proteins.
• Some enzymes are simple and others have multiple polypeptide subunits.
• Most enzymes require cofactors (ions or organic molecules) for activity: these cofactors are in the active site
• Some biological catalysts are built from RNA, called ribozymes.
• The active site of an enzyme is a region where substrates bind and catalyze reactions.
• Induced fit of the substrate brings groups closer, making enzymes more efficient.

Lowering the EA Barrier

• The active site lowers the activation energy barrier needed for reactions.
• The active site changes the substrate into a more favorable state for the reaction and the breaking of bonds
• The active site orients the substrates correctly
• The active site strains substrate bonds
• The active site provides a favorable microenvironment
• The active site forms covalent bonds temporarily with the substrate

Enzyme Activity and Regulation

• Enzyme activity can be affected by environment, pH, optimal conditions and temperature. A specific temperature is best for catalysis in the enzyme's environment.

Cofactors and Regulation

• Cofactors are non-proteins that help enzymes function. These include inorganic molecules such as magnesium.
• Coenzymes are organic molecules, often vitamins
• Enzymes without cofactors are called apoenzymes, and are inactive.
• Enzymes with cofactors are called holoenzymes.

Enzyme Inhibitors

• Competitive inhibitors bind to the active site, blocking substrates from binding.
• Noncompetitive inhibitors bind to a site other than the active site, causing a conformational change that lowers the effectiveness of the enzyme
  • Irreversible inhibitors covalently bind to the enzyme, permanently inhibiting it.
  • Allosteric inhibitors bind to the allosteric site and change the conformation of the enzyme, decreasing the ability of the enzyme to function optimally.
• Allosteric activators bind to the allosteric site; the shape changes into a more favourable configuration for the reaction to occur

Enzyme Allosterism

• Some enzymes have multiple subunits
• Enzyme activators and inhibitors bind to allosteric sites, altering the enzyme shape and thus its activity or ability to function.
• Activator = shape change to an active form
• Inhibitor = shape change to an inactive form
• Cooperativity—a substrate binding to one enzyme subunit can enhance the binding of substrates to other subunits.

Enzyme Feedback

• In feedback inhibition, the end product of a metabolic pathway regulates its own production by inhibiting an enzyme involved in an earlier step, preventing an overproduction of the end product.
• Iso/glutamine conversion

Enzyme Compartmentalization

• Structures within cells help order metabolic pathways.
• Some enzymes are structural components of membranes or organelles
• Enzymes related to respiration are in mitochondria, and digestive enzymes are in lysosomes.

Activation Energy Extra Credit Discussion

• Activation energy describes the energy needed to overcome a barrier in chemical reaction, or the initial energy required for a reaction to occur.
• Catalyst reduce activation energy requirements = increases reaction rates