12-06: Enzymes

What are Enzymes?

• Biological catalysts: proteins that speed up metabolic reactions by lowering energy barriers

• Assist in chemical reactions, but are not used up in the reaction

• They lower the activation energy (minimum amount of energy required to initiate a reaction) of the reaction

• Many names end in -ase (e.g. lactase, amylase, etc)

  

  

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Enzymes and Substrates

• Enzymes are substrate specific

  • They depend on the enzyme’s 3D shape (remember that structure determines function) - though enzymes are as well flexible

• An enzyme binds to its substrate and catalyzes its conversion to product

  • Substrate: the substance an enzyme acts on & makes more reactive

• The substrate binds to the enzyme’s active site

  

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Models for Enzymes

• Originally was the lock and key model → idea that it had to fit in like a key into a lock
• Now updated to the induced fit model → the enzyme hugs the substrate and isn’t rigid but still has to be a close enough fit

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How Enzymes Work

• Distorts the substrate’s chemical bonds so less energy is needed
• Provides a micro environment that is more ideal for the chemical reaction (e.g. pH)
• Side chains of amino acids can be positioned to participate in the reaction and can help with the reactivity - there to break the bonds within the substrates imitates the reaction to occur more readily

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Reaction Rates

• Concentration of substrate plays a role in reaction speed

• More substrate = faster reaction, until it reaches the point of being saturated

  • Enzyme saturated: all enzyme are being used to reaction rate plateaus (if all active sites are occupied)
  • With enzyme saturation, the rate of reaction is determined by the rate the active site converts substrates into products

  

Optimal Conditions

• A cell’s physical & chemical environment impacts enzyme activity
• Each enzyme has optimal environmental conditions that favour the most active enzyme conformation (the enzyme works best when its in its favourite shape and environment)
• Temperature and pH impact the enzyme
  • Optimal temperature allows the greatest number of molecular collisions without denaturing the enzyme - heat makes collisions increase but if there is too much heat, it will denature the enzymes → the optimal temperature for most human enzymes is 35ºC - 40ºC
• Optimal pH for most enzymes is 6-8 but some will operate at more extremes of pH (like digestive enzymes; pepsin is lower and trypsin is higher in pH)

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Cofactors

• Sometimes enzymes don’t work even in optimal conditions - they need the help of cofactors and coenzymes to help catalyze reactions
• They may bind tightly to the active site or loosely to both active site and substrate - allowing the enzyme to function
• Cofactors: small nonprotein (e.g. metal atoms of zinc, iron, copper)
• Coenzymes: organic molecules (e.g. vitamins)

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Inhibitors

• There are molecules that bind to enzymes to make them less effective
• 2 types of inhibitors: competitive and noncompetitive inhibitors

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Competitive Inhibition

• Competitive inhibitors: molecules that bind reversibly or irreversibly to the active site
  • Compete with the substrate for space in the active site
• Reversible: looks similar and behaves similarly to the substrate, when the competitor is in high concentration to inactivates the enzyme by outcompeting the substrate - reversible as the competitor can be overwhelmed by high concentrations of substrate
• Irreversible: the competitor occupies the active site permanently and therefore deactivate the enzyme, e.g. carbon monoxide is an irreversible competitive inhibitor of hemoglobin which competes with oxygen
• Most naturally occurring inhibitors are irreversible

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Non-competitive Inhibition

• The inhibitor reacts with the allosteric site (some other place on the enzyme that isn’t the active site), changing the shape of its active site
• If the shape is altered then the substrate can’t bond to it
• Reversible (allosteric control): used to regulate metabolic pathways in the cell (series of chemical reactions required for a specific product)
  • The final product molecule acts as inhibitors to enzymes earlier in the pathway (typically the first)
  • This is called negative feedback (giving info to stop something from happening)
  • Negative feedback prevents runaway reactions and overproduction of products
• Irreversible: bind irreversibly wth some other part of the enzyme and permanently denature/inactivate it
  • Permanently alter the native conformation of the protein (e.g. cyanide inhibits cytochrome c oxidase and effectively blocks cellular respiration causing the organism to die)

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Control of metabolism

• Allosteric enzymes have 2 conformations - one catalytically active and the other inactive
• Binding of an activator to an allosteric site stabilizes the active conformation
• Binding of an inhibitor to an allosteric site stabilizes the inactive conformation
• Enzyme activity changes continually in response to changes in the relative proportions of activators and inhibitors

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