Enzyme Action (DP IB Biology)

Structure of Enzymes

The structure of enzymes

• 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

Enzyme action diagram

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 3D shape of the protein that makes up the enzyme

  • The active site is made of only a few amino acids but the interaction of these amino acids within the 3D shape of the enzyme ensures that catalysis can occur

  • This is achieved by:

    • Binding to the substrate molecule

    • Holding it in position for a chemical reaction to occur

    • Lowering the energy needed for the reaction to occur 

Enzyme specificity diagram

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

Formation of enzyme-substrate complex diagram

The temporary formation of an enzyme-substrate complex

Induced-fit Binding

The induced-fit hypothesis

• The original model explaining interactions between enzymes and their substrate molecules was called the lock-and-key model

  • This model proposed that the enzyme active site is precisely complementary to the shape of the substrate molecule

  • The substrate molecule therefore fits into the active site like a key in a lock

• The modified model of enzyme activity is known as the ‘induced-fit hypothesis’

• Although it is very similar to the lock and key hypothesis, in this model the enzyme and substrate interact with each other:

  • The enzyme and its active site (and sometimes the substrate) can change shape slightly as the substrate molecule enters the enzyme

  • These changes in shape are known as conformational changes

  • This ensures an ideal binding arrangement between the enzyme and substrate is achieved

  • This maximises the ability of the enzyme to catalyse the reaction

Induced-fit model diagram

The induced-fit hypothesis of enzyme action

Enzyme Catalysis

The role of molecular motion and substrate-active site collisions

• In order for the substrate molecule to collide with and ultimately bind to the enzyme active site, movement is required

  • This movement is the result of the kinetic energy that molecules have

  • The greater the kinetic energy of the molecules, the faster the movement and the higher the probability of enzyme and substrate colliding

  • This leads to more enzyme-substrate complexes forming and the production of more product molecules

• In some cases, large substrate molecules are immobilised, while in other cases it is possible to immobilise enzymes by embedding them in membranes

• These immobilised enzymes can be used in a range of industries such as food processing, environmental management, pharmaceuticals and manufacturing processes

• There are different methods by which enzymes can be immobilised including:

  • Attachment to an inert substance e.g. glass

  • Entrapment within a matrix e.g. alginate gel

  • Entrapment within a partially permeable membrane

Examples of immobilised enzymes diagram

There are many different ways in which enzymes can be immobilised

Advantages of immobilised enzymes

• There is no enzyme in the product (the product is uncontaminated) and therefore there is no need to further process or filter the end product

• The immobilised enzyme can be reused multiple times which is both efficient and cost-effective (many enzymes are expensive)

  • Reusing the enzyme also avoids the need to separate the enzyme from the product in downstream processing

• Immobilised enzymes have a greater tolerance of temperature and pH changes (immobilisation often makes enzymes more stable)

• Substrates can be exposed to higher enzyme concentrations than when using enzymes in solution, increasing the rate of throughput

• Conditions can be controlled carefully, allowing immobilised enzymes to function close to their optimum conditions and be more stable

Denaturation: Enzymes

• Enzymes can be denatured when it is exposed to high temperatures or extremes of pH

• Bonds (e.g. hydrogen bonds) holding the enzyme molecule in its precise 3D shape start to break

  • Take note that the peptide bonds holding the amino acids together are not broken

• This causes the 3-dimensional shape of the protein (i.e. the enzyme) to change

• This permanently changes the shape of 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 between the R-groups of amino acids so they start to break, changing the conformation of the enzyme