Enzymes

• Enzymes are globular proteins that act as the body's catalysts. They speed up time for reactions to reach equilibrium, and lower the activation energy of a reaction.


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• Enzymes lower the activation energy without changing the total energy difference (delta g).


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• Catalysts can

  • Provide a reaction surface (active site makes it easier for reactants to bind)
  • Provide a suitable environment (hydrophobic/lipophilic)
  • Bring reactants together into closer proximity
  • Orient/position reactants correctly for reaction
  • Weaken reactant bonds
  • Provide acid/base catalysts --> think amino acids
  • Provide nucleophilic groups --> donate electrons
  • Stabilise the transition state with intermolecular bonds --> keeps products
• Most enzymes have an 'active site' which is a hydrophobic cleft or hollow on its surface. This accepts reactants (substrates and cofactors). It contains amino acids which bind the reactants together, and participate in the enzyme-catalysed reaction.
• There aqre three types of forces, Ionic, H-bonding, and van der Waals (dispersion)
• With substrate binding, the active site is nearly the correct shape for the substrate. Binding alters the enzyme's shape to maximise intermolecular bonding, called an 'induced fit'. This can strain bonds in the substrate, making the reaction proceed faster. This Binding involves intermolecular bonds between functional groups in the substrate and functional groups in the active site.

  
• Pyruvic acid --> has a hydrogen bond at green, vdw at orange, ionic at purple

  
• For chymotrypsin (digestive enzyme produced in the pancreas), it uses multiple mechanisms. The catalytic triad of serine, histidine, and aspartate work together. Serine acts as a nucleophile, histidine acts as an acid/base catalyst, and aspartate orientates the histidine.
• Polar serine breaks the pi bond, creating a new transient covalent bond with carbon, fragmenting the protein into more digestible chunks. Aspartame orients the histamine with a hydrogen bond so that it is at the correct orientation to act as a base, accepting the hydrogen from serine to become an acid.

  
• With chymotrypsin, an oxyanion hole is formed in the region of the active site occupied by the negatively charged oxygen of the tetrahedral intermediate. This oxyanion is stabilised by hydrogen bonds to peptide bonds close by. This interaction stabilises the transition state leading to the oxyanion intermediate and thus lowers the activation energy.

  
• Binding interactions must be strong enough to hold the substrate sufficiently long for the reaction to occur. They must also be weak enough to allow the product to depart. Interactions stabilise the transition state. Designing molecules with stronger binding interactions results in enzyme inhibitors which block the active site.

  
• A nucleophile is a reactant that donates a pair of electrons to form a new covalent bond
• Many enzymes are regulated by intracellular agents, that either enhance or inhibit the enzyme. The products of some enzyme-catalysed reactions may act as inhibitors to then slow production, called a reverse feedback loop. Usually binding to a binding site is called an allosteric binding site.
• Inhibitors bind reversibly to allosteric binding sites, forming intermolecular bonds. The induced fit alters the shape of the enzyme to distort the active site, making it unrecognisable to substrates. Increasing substrate concentration won't affect this. The inhibitor differs in structure to the substrate.

  
• Enzymes with allosteric sites are often at the start of biosynthetic pathways. The enzyme is controlled by the final product of the pathway. This binds to the allosteric site and switches off the enzyme. Drugs acting as enzyme inhibitors can be designed to target the active site or the allosteric site.

  
• External signals can also regulate the activity of enzymes (eg neurotransmitters and hormones). Chemical messengers will initiate a signal cascade that activates protein kinases (a different enzyme type). Protein kinases phosphorylate target enzymes to affect activity.

  
• Reversible inhibitors bind reversibly to the active site. They use intermolecular bonds, and no reaction. Inhibition depends on the strength of inhibitor binding and concentration. They block the substrate from the active site, but increasing substrate concentration reverses inhibition. They are likely to be similar in structure to the substrate, product or cofactor.
• Irreversible inhibitors form a covalent bond between the drug and the enzyme, this blocks the substrate from the active site. Increasing substrate concentration does not reverse inhibition. It is likely to be similar in structure to the substrate.

  
• Orlistat is an irreversible inhibitor that inhibits pancreatic lipase, making it an anti-obesity drug. The enzyme is blocked from digesting fats in the intestine, leading to reduced biosynthesis of fat in the body as fatty acids and glycerol cannot be as effectively absorbed.
• Allosteric inhibitors bind reversibly to the allosteric site via intermolecular bonds. They mimic natural allosteric inhibitors made in biosynthetic pathways. This induced fit alters the shape of the enzyme. The active site is distorted and is not recognised by the substrate. Increasing substrate concentration does not reverse inhibition. It is not similar in structure to the substrate.

  
• Transition-state inhibitors mimic the transition state of an enzyme-catalyse reaction. They are likely to bind more strongly than drugs mimicking the substrate or product. They are high energy, transient species that cannot be isolated or synthesised. We design these drugs based on reaction intermediates which are closer in character to the transition state we're trying to copy. It mimics the stereochemistry and binding properties of the reaction intermediate, but it is stable, so it won't go on to do the product's role in the body.
• Renin inhibitors block synthesis of angiotensin I and II. These constrict blood vessels and raise blood pressure, so renin inhibitors act as antihypertensives (blood pressure medication). Renin is formed by two aspartyl residues creating a tetrahedral intermediate. Using aliskiren, the hydroxyethylene transition-state mimic copies the geometry of the reaction intermediate. This remains stable as part of the larger molecule and so no leaving group presents.

  
• Suicide substrate are agents which are converted into irreversible inhibitors by the enzyme-catalysed reaction. They react with the target enzyme once formed. Initially Tienilic acid was marketed as a diuretic, but withdrawn due to its interaction with cytochrome P450 enzymes, where it forms an intramolecular bond, rendering the enzyme alkylated and inhibited - irreversible.
• long distance signalling through the bloodstream is endocrine signalling. Short distance signalling is the paracrine signalling, using paracrine factors.
• Autocrine process is when the ligands released from the vesicles bind with receptors on the same cell, so it is self-signalling.
• latching on at the receptor = signal perception
• when the protein changes its shapes, catalyses a reaction, or inhibits a reaction, that is signal transduction, which creates a cellular response