8.2 Applications and skills

8.2.1 Enzyme inhibition and rates of reaction

  • Metabolic pathways can be manipulated for different purposes.  One way to alter a metabolic pathway is to introduce an inhibitor. Another way is to continuously extracting product to encourage overdevelopment of a specific metabolite.
  • Many pharmaceuticals, including antibiotics, work by altering the metabolic pathways in disease-causing organisms. Bioinformatics makes it easier to determine which enzymes to target.

Application: Use of databases to identify potential new anti-malarial drugs

  • Malaria is caused by a number of species of micro-organism of the genus Plasmodium, especially Plasmodium falciparum. These protozoans live as sporozoites in the gut of the female Anopheles mosquito, and are transmitted via bites to a human host. The parasite then develops, rupturing hepatocytes and infecting erythrocytes, and causing weakness, chills, fever, vomiting and seizures.

Figure 8.2.1a – Life cycle of PlasmodiumFigure 8.2.1a – Life cycle of Plasmodium

  • In 2002, a complete genome for Plasmodium falciparum strain 3D7 was sequenced. The existence of the database can help researchers locate enzymes that could be inhibited in anti-malarial drugs.

Figure 8.2.1b – Summary of chemogenomic profile for Plasmodium falciparum: a) Identified genes b) Mechanism of drug action c) Efficacy curveFigure 8.2.1b – Summary of chemogenomic profile for Plasmodium falciparum: a) Identified genes b) Mechanism of drug action c) Efficacy curve

  • They could also test different drugs on mutant strains of Plasmodium and determine, using the database, which genes are associated with altered responses to the drugs.  This type of research is called chemogenomics.

Skill: Distinguishing different types of inhibition from graphs at specified substrate concentration.

Reaction rates can be altered by competitive or non-competitive inhibition of enzymes. Consider the following generalised graphs demonstrating the effects of two types of enzyme inhibitors:

Figure 8.2.1c – The effect of inhibition on reaction rates at different substrate concentrationsFigure 8.2.1c – The effect of inhibition on reaction rates at different substrate concentrations

1. Explain the trend between substrate concentration and reaction rate. (2 marks)

  • The reaction rate increases as the substrate concentration increases, until the maximum rate of reaction is achieved. The rate of reaction then reaches a plateau, and increases no further.
  • The reaction rate is limited at low concentrations by the availability of substrate, while at high concentrations, the rate is limited by the availability of enzyme active sites.

2. Compare and contrast the effects of inhibitors A and B. (2 marks)

  • Both inhibitor A and inhibitor B lower the reaction rate at low substrate concentrations.
  • Inhibitor B lowers the maximum reaction rate, while inhibitor A does not.

3. Deduce the type of inhibition shown by inhibitors A and B. (2 marks)

  • Inhibitor A is competitive – when the concentration of substrate begins to exceed the concentration of inhibitor, the maximum rate of reaction can be achieved because the substrate has a higher chance of accessing active sites.
  • Inhibitor B is non-competitive – non-competitive inhibitors bind to another site on the enzyme, and make the active site inaccessible. Increasing the substrate concentration does not decrease the inhibiting effect.

Skill: Calculating and plotting rates of reaction from raw experimental results.

A student tested the effect of hydrogen peroxide concentration on catalase activity in potato cells, using the following apparatus:

Figure 8.2.1d – Catalase activity in potato cellsFigure 8.2.1d – Catalase activity in potato cells

He performed five trials and averaged his results.

Figure 8.2.1e – Catalase activityFigure 8.2.1e – Catalase activity

  1. Use a spreadsheet program (i.e. Excel) to plot the results for each percentage of H2O2. Download the raw data here.
  2. Calculate the maximum rate of reaction, and the average rate of reaction at each percentage of hydrogen peroxide, in cm3s-1.

Figure 8.2.1f – Anopheles mosquitoFigure 8.2.1f – Anopheles mosquito
Malaria is transmitted by mosquito bites, and kills about one million people every year.

Key skills

  • Discuss the use of bioinformatics in drug design.
  • Distinguish between competitive and non-competitive enzyme inhibition.
  • Calculate and plot rates of reaction from raw data.

Figure 8.2.1g – Musical chairsFigure 8.2.1g – Musical chairs
Competitive inhibition is like musical chairs. Who will get there first?

Figure 8.2.1h – Smashing chairFigure 8.2.1h – Smashing chair
Non-competitive inhibition is not like musical chairs. There is no chair!

Exam tip

When you are asked to:

  •  explain a graph or trend, always provide a description of the trend first, then explain it using appropriate terminology.
  • compare and contrast two items, always refer to both in the same sentence.

Figure 8.2.1i – StopwatchFigure 8.2.1i – Stopwatch

IA

A rate of reaction should be expressed as a ratio. For example:

  • volume of gas collected over time (cm3/min)
  • mass of substrate lost over time (mg/hour).

Students often forget to include the time, or rate, aspect in their IAs.

Nature of Science

Developments in scientific research follow improvements in computing. Bioinformatics has facilitated research into metabolic pathways.

Course link

  • The sickle cell phenotype is correlated to malaria resistance. See 3.2.1.
  • Pathway engineering is discussed in Option B: 13.1.1.

Further reading

(image available from creative commons. Can you use it without modification?”)Chemogenomic profiling of Plasmodium falciparum as a tool to aid antimalarial drug discovery

Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4635350/

Downloads

Excel workbook 8.2.1 Excel | PDF