M8. Enzymes are specific for their substrate.

Student Outcome: M8.1

Describe the induced-fit model of enzyme–substrate binding.

The induced-fit theory assumes that the substrate plays a role in determining the final shape of the enzyme and that the enzyme is partially flexible. This explains why certain compounds can bind to the enzyme but do not react because the enzyme has been distorted too much. Other molecules may be too small to induce the proper alignment and therefore cannot react. Only the proper substrate is capable of inducing the proper alignment of the active site.

The diagram shows the substrate (yellow) fitting into the active site of the enzyme (blue). In the second diagram, a reaction has occured in the substrate and enzyme, cleaving the substrate. In the final diagram, two new products have formed.

Video on how the Induced Fit Model works

This video has an advertisement at the beginning but the graphics are awesome. It is over 8 minutes long but worth it.

A really nice (but lengthy) summary of the basics of how enzymes work here (from Scientific American Blogs)

Student Outcome: M8.2

Explain how pH, temperature, and chemical inhibitors can alter the binding of enzymes and substrates at the active site.

Temperature

Higher temperature generally causes more collisions among the molecules and therefore increases the rate of a reaction. More collisions increase the likelihood that substrate will collide with the active site of the enzyme, thus increasing the rate of an enzyme-catalyzed reaction.

Above a certain temperature, activity begins to decline because the enzyme begins to denature.

The rate of chemical reactions therefore increases with temperature but then decreases as enzymes denature.

pH

Each enzyme has an optimal pH.

A change in pH can alter the ionisation of the amino acids. When the charges on the amino acids change, hydrogen bonding within the protein molecule change and the molecule changes shape. The new shape may not be effective.

Source: http://faculty.clintoncc.suny.edu/faculty/Michael.Gregory/files/Bio%20101/Bio%20101%20Laboratory/Enzymes/Enzymes.htm

  This graph shows how the optimum temperature of enzymes can be different.

Inhibitors

Just as it is important for enzymes to catalyze biological reactions, so is the ability to control and regulate enzymatic activity. This is the role of small, specific molecules and ions known as enzyme inhibitors. Inhibitors are often molecules that are similar in shape to a certain substrate and can thus fit the active site of the enzyme that was intended to fit the substrate. Once the inhibitor occupies the active site, however, it does not act to catalyze the reaction as the enzyme would. Instead, it binds up the active site and does not allow any activity there; thus, the reaction is inhibited.

Enzymes can also be inhibited, usually negatively, by drugs and toxic agents. Inhibition can even occur as a result of the enzymes producing too many product molecules. Enzyme inhibitors are classified as either reversible or irreversible.

Reversible Inhibitors

The main characteristic of reversible inhibitors is the fact that they disassociate very quickly from the enzyme substrate after they attach to form an enzyme-inhibitor complex. In competitive inhibition, a form of reversible inhibition, an enzyme is kept from being able to form an enzyme-substrate (ES) complex and thus can not complete the task of catalyzing the reaction. Enzymes can form ES complexes or enzyme-inhibitor (EI) complexes, but not enzyme-substrate-inhibitor (ESI) complexes. In order to form an enzyme-inhibitor complex, many inhibitors take on a shape that is very similar to the substrates. They then bind to the enzyme at the active site which prevents the substrate from binding at the site.

Competitive Inhibition

Since ESI complexes can not be formed, the active site with the inhibitor attached essentially becomes useless. Simply put, a competitive inhibitor reduces the rate at which the catalyst can work by reducing the number of enzyme molecules bound to a substrate. One way to overcome competitive inhibition is to increase the concentration of the substrate

Another type of reversible inhibition is known as noncompetitive inhibition. In this type of inhibition, the inhibitor binds to the enzyme at a site other than the active site. In doing so the inhibitor changes the shape of the active site so that the substrate no longer fits it. Again, the result is the substrate can not come in contact with the active site and the enzymatic action can not occur. Non- competitive inhibition can not be overcome by increasing the concentration of the substrate.

Here is a video using Halo characters to represent the different aspects of this idea - note: I don't endorse the violent behaviour but will let it pass in the name of science.

Source: http://stezlab1.unl.edu/reu1999/dputn226/ChemHelp/RET_Web_Pages/Enzyme_inh/enz_ihb2.htm

Here is a very interesting series of animations showing things like inhibition. There is even an interactive version - scroll near the bottom of the page.