Enzymes (DP IB Biology: HL)

• Enzymes are biological catalysts
  • ‘Biological’ because they function in living systems
  • ‘Catalysts’ because they speed up the rate of chemical reactions without being used up or changed themselves
  • Enzymes have an active site to which specific substrates bind

• Enzymes are also globular proteins
• Critical to the enzyme's function is the active site where the substrate binds
• Enzymes are specific to the substrate
  • The shapes of the enzyme and substrate and their chemical properties are complementary, to allow the substrate to fit into the active site, like two jigsaw pieces fitting together
  • This is called enzyme-substrate specificity

• Due to this specificity, thousands of enzymes are needed throughout an organism, to carry out individual chemical reactions

• Enzyme catalysis involves molecular motion and the collision of substrates with the active site
• For an enzyme-catalysed reaction to take place, substrates collide at random with the enzyme's active site
• This must happen at the correct orientation and speed in order for a reaction to occur
  • Unsuccessful collisions can occur when the molecules are not correctly aligned with each other at the moment of collision
  • The molecules 'bounce' off each other and no reaction takes place

• Some enzymes have two substrates that must each collide with a separate active site at the same time
• Substrates bind to enzymes, forming a temporary enzyme-substrate complex
• The active site of an enzyme has a specific shape and chemical properties to bind with a specific substrate
• The reaction occurs within the enzyme-substrate complex which leads to changes in the chemical structure of the substrate
• Products are formed, which detach and move away from the active site, which can be re-used

The active site of an enzyme has a specific shape to fit a specific substrate (when the substrate binds an enzyme-substrate complex is formed)

• The specificity of an enzyme is a result of the complementary nature between the shape of the active site on the enzyme and its substrate(s)
• The shape of the active site (and therefore the specificity of the enzyme) is determined by the complex 3-D shape of the protein that makes up the enzyme
  • Proteins are formed from chains of amino acids held together by peptide bonds
  • The order of amino acids in this chain determines the shape of an enzyme
  • If the order is altered, the resulting three-dimensional shape changes

An example of enzyme specificity – the enzyme catalase can bind to its substrate hydrogen peroxide as they are complementary in shape, whereas DNA polymerase is not

The temporary formation of an enzyme-substrate complex

• Enzyme reactions can either be catabolic or anabolic
• Catabolic reactions involve the breakdown of complex molecules into simpler products, which happens when a single substrate is drawn into the active site and broken apart into two or more distinct molecules
• Examples of catabolic reactions include cellular respiration and hydrolysis reactions

A catabolic reaction

• Anabolic reactions involve the building of more complex molecules from simpler ones when two or more substrates are held in the active site, forming bonds between them and releasing a single product
• Examples of anabolic reactions include protein synthesis and photosynthesis

An anabolic reaction

• Temperature, pH and substrate concentration affect the rate of activity of enzymes
• Enzymes have a specific optimum temperature – the temperature at which they catalyse a reaction at the maximum rate
• Lower temperatures either prevent reactions from proceeding or slow them down:
  • Molecules move relatively slowly
  • Lower frequency of successful collisions between a substrate molecule and the active site of enzyme
  • Less frequent enzyme-substrate complex formation
  • Substrate and enzyme collide with less energy, making it less likely for bonds to be formed or broken (stopping the reaction from occurring)

• Higher temperatures speed up reactions:
  • Molecules move more quickly
  • Higher frequency successful collisions between a substrate molecule and the active site of enzyme
  • More frequent enzyme-substrate complex formation
  • Substrate and enzyme collide with more energy, making it more likely for bonds to be formed or broken (allowing the reaction to occur)

• However, as temperatures continue to increase, the rate at which an enzyme catalyses a reaction drops sharply, as the enzyme begins to denature

The effect of temperature on the rate of an enzyme-catalysed reaction

Changes in pH

• pH is a result of the hydrogen ion concentration in a solution
• A low pH is acid and has a high hydrogen ion concentration
• A high pH is alkaline and has a low hydrogen ion concentration
• A 10× increase in hydrogen ion concentration lowers the pH by 1 unit
  • pH is therefore measured on a logarithmic scale of hydrogen ion concentration, not a linear scale

• Water has a pH of 7, regarded as neutral
• Extremes of pH can also alter hydrogen bonding within an enzyme's structure and cause irreversible denaturation
• Each enzyme has an optimum pH
• Not all enzymes have an optimum pH near to neutral. For example
  • The stomach enzyme pepsin is adapted to work best at pH 2
  • Certain bacterial enzymes work at pH 9-10, in line with the pH of the bacteria's main habitat

The effect of pH on three enzymes' rates of reaction

Changes in substrate concentration

• The more substrate molecules are present in a solution, this increases the frequency of collisions with the enzyme's active site
• Active sites are occupied or 'blocked' by substrates whilst the reaction is taking place
• The more active sites are occupied, the fewer are available to catalyse other substrate molecules
• As substrate concentration rises, the slower the rise in the rate of the enzyme-catalysed reaction
• The active sites have become saturated
• At the point of active site saturation, increasing the substrate concentration will cause no further increase in the rate of reaction
• At the point of active site saturation, a method of increasing the rate of reaction would be to make more active sites available by increasing the enzyme concentration

The effect of substrate concentration on enzyme activity

• Enzymes can be denatured
• High temperatures and extremes of pH cause denaturation
• Bonds (eg. hydrogen bonds) holding the enzyme molecule in its precise 3D shape start to break
• This causes the 3-dimensional shape of the protein (ie. the enzyme) to change
• This permanently damages the active site, preventing the substrate from binding
• Denaturation has occurred if the substrate can no longer bind
• The reaction that was previously catalysed now no longer takes place
• Denaturation often causes the enzyme to become insoluble and form a precipitate
• Very few human enzymes can function at temperatures above 50°C
  • This is because humans maintain a body temperature of about 37°C, therefore even temperatures exceeding 40°C will cause the denaturation of enzymes
  • High temperatures cause increased vibrations in the bonds and the hydrogen bonds between amino acids start to break, changing the conformation of the enzyme