Enzymes and Catalysis Study Guide

Properties of Catalysts and How Enzymes Function

• Catalysts increase reaction rate without changing the reaction's nature or being altered by the reaction.
• Enzymes are protein catalysts that speed up specific chemical reactions.
• Enzymes lower the activation energy required for a reaction to proceed.
• Non-catalyzed reactions occur without an enzyme (e.g., amylase).
• Catalyzed reactions occur when an enzyme is present.

How Enzymes Catalyze Chemical Reactions

• Enzymes lower activation energy, allowing more reactants to participate and increase the reaction rate.
• Catalysts enable faster reactions at lower temperatures by reducing the required activation energy.
• Enzymes' ability to lower activation energy results from their structure.
• Enzymes are large proteins with complex 3D shapes formed by interactions between amino acid subunits.
• Each enzyme has a unique 3D conformation with ridges, grooves, and pockets lined with specific amino acids.
• Active sites are pockets within enzymes that catalyze reactions.
• Substrates have specific shapes that allow them to fit into the active site (lock-and-key model).
• Mechanism of action:
  1. Substrates fit into active sites.
  2. Enzyme-substrate complex forms.
  3. Reaction occurs.
  4. Products dissociate.
  5. Enzyme remains unaltered.

Enzyme Naming

• Enzyme names typically end with the suffix "-ase", except for some older enzymes like pepsin, trypsin, and renin.
• Enzyme classes are named according to their activity or "job category".
  • Hydrolases catalyze hydrolysis.
  • Phosphatases catalyze the removal of phosphate groups.
  • Synthases and synthetases catalyze dehydration synthesis reactions.
  • Dehydrogenases remove hydrogen atoms from substrates.
  • Kinases add phosphate groups to molecules.
  • Isomerases rearrange atoms within substrate molecules to form structural isomers (e.g., glucose and fructose).

Effects of pH and Temperature on Enzyme Activity

• The rate of enzyme-catalyzed reactions depends on enzyme concentration, pH, and temperature.
• Increasing temperature increases the rate of non-enzyme-catalyzed reactions.
• Enzyme reactions also increase with temperature, but only up to a point.
• At 0°C, the reaction rate is very slow.
• As temperature increases above 0°C, the reaction rate increases until it reaches a plateau a few degrees above body temperature (37°C).
• Further increases in temperature decrease the reaction rate due to the altered tertiary structure of enzymes at high temperatures (protein denaturation, causing loss of function).
• An enzyme's pH optimum usually reflects the pH of the body fluid where it's found.
  • Pepsin's acidic pH optimum allows it to be active in the strong hydrochloric acid of gastric juice.
  • Salivary amylase has a neutral pH optimum.
  • Trypsin has an alkaline pH optimum in pancreatic juice, allowing it to digest starch and protein in other parts of the alimentary canal.
• Enzyme activity is the rate at which substrates are converted to products. Higher enzyme concentration leads to increased activity (increased rate).

Inactive Enzyme Forms, Activation, and Second Messengers

• Many enzymes are produced in an inactive form.
  • Pancreatic digestive enzymes are activated only when they reach the intestine to protect the pancreas from self-digestion.
• Some enzymes are activated by phosphorylation (adding phosphate) and inactivated by dephosphorylation (removing phosphate).
• Others are activated by ligands (small molecules) called second messengers.

Cofactors and Coenzymes

• Cofactors are ions and smaller organic molecules needed for the activity of specific enzymes.
• Cofactors include metals (Ca²⁺, Mg²⁺, Mn²⁺, Cu²⁺, Zn²⁺, Se).
• Some enzymes require cofactors to have a properly shaped active site. Binding of the cofactor causes a conformational change in the protein that allows it to combine with the substrate.
• Aids in temporary bonding between enzyme and substrates.
• Coenzymes are organic molecules derived from water-soluble vitamins (e.g., niacin and riboflavin) needed for enzyme function.
• Coenzymes participate in enzyme-catalyzed reactions by transporting hydrogen.
• They act as "taxi cabs" to transport molecules to the next reaction in the metabolic pathway.

Effect of Substrate Concentration

• As substrate concentration increases, the rate of product formation increases until the reaction rate reaches a plateau where enzymes are saturated.

Law of Mass Action in Reversible Reactions

• Some enzymatic reactions within a cell are reversible, with both the forward and backward reactions catalyzed by the same enzyme.
• Law of mass action: reversible reactions will be driven from the side of the equation where the concentration is higher to the side where the concentration is lower.
• Example: Carbonic anhydrase
  • H2CO3 \rightleftharpoons H2O + CO2
  • H2O + CO2 \rightleftharpoons H2CO3
  • Conveniently illustrated: H2O + CO2 \rightleftharpoons H2CO3

Metabolic Pathways, End-Product Inhibition, and Inborn Errors

• Metabolic pathways are sequences of enzymatic reactions that start with an initial substrate, progress through intermediates, and end with a final product.
• The product of one enzyme becomes the substrate for the next enzyme, like workers on an assembly line.
• End-product inhibition:
  • The activities of enzymes at branch points of metabolic pathways are often regulated by end-product inhibition (a form of negative feedback).
  • Occurs when a product in a divergent pathway inhibits the activity of the branch-point enzyme.
  • Prevents final product accumulation.
  • Causes the reaction to favor an alternate pathway.
• Occurs by allosteric inhibition: the mechanism by which a final product inhibits an earlier enzymatic step in its pathway.
  • This causes a conformational change of the enzyme protein, resulting in a change in the shape of the active site, so it can no longer combine properly with its substrate.
• Inborn errors of metabolism: inherited defects in a gene that codes for a polypeptide.

Endergonic vs. Exergonic Reactions & ATP

• Endergonic reactions require an input of energy to proceed; products contain more free energy than reactants.
• Exergonic reactions release energy as the process occurs; products contain less free energy than reactants.
• The energy released by most exergonic reactions in the cell is used to drive the formation of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) and inorganic phosphate.
• The formation of ATP requires a significant amount of energy to be conserved.
• Adenosine\ diaphosphate(ADP) + inorganic\ phosphate(Pi) \rightarrow ATP

Oxidation and Reduction Reactions; NAD and FAD

• When an atom or molecule gains electrons, it is reduced; when it loses electrons, it is oxidized.
• Reduction and oxidation are always coupled reactions: an atom or molecule cannot be oxidized unless it donates electrons to another, which is then reduced.
• Oxygen acts as the final electron acceptor in a chain of oxidation-reduction reactions that provide energy for ATP production.
  • If a molecule gains electrons, it is reduced.
  • If a molecule loses electrons, it is oxidized.
  • A reducing agent donates electrons.
  • An oxidizing agent accepts electrons.
• Coenzymes function as hydrogen carriers because they accept hydrogens (becoming reduced) in one enzyme reaction and donate hydrogens (becoming oxidized) in a different enzyme reaction.
  • Nicotinamide adenine dinucleotide (NAD): derived from the vitamin niacin (Vit B3).
  • Flavin adenine dinucleotide (FAD): derived from the vitamin riboflavin (Vit B2).

Enzymes and Energy Release

• Enzymes do not change the amount of energy released; they increase the reaction rate.

Temperature and Enzyme Function

• Enzymes can become denatured if they get too hot.

Mechanisms of Controlling Enzyme Activity

1. Covalent modification: Phosphorylation of receptors or enzymes.
   • Activates or inactivates a response.
2. Allosteric modulators: cofactors (bind to a site other than the activation site).
   • Enables or inhibits a reaction.
3. End-product inhibition: a special case of allosteric inhibition.
   • The product binds to the allosteric site of an enzyme in an earlier part of the pathway.
4. Competitive inhibition: binds to the active site on the enzyme or a binding site on the receptor.
   • Inhibits (decreases) activity.

Oxidizing Agent, FAD, and FADH₂

• Each FAD can accept 2 electrons and bind 2 protons.
• The reduced form of FAD is combined with the equivalent of 2 hydrogen atoms and may be written as FADH₂.

Effect of Substrate Concentration on Enzyme Rate

• Figure 4.6 illustrates the effect of substrate concentration on enzyme rate.