DNA-lab “Bioinformatics: a bit of life”

Identify a mystery protein using its amino acid sequence and function. Combine all the findings in a spatial model and experiment in three dimensions.

For a couple years now, we know the sequence of the three billion bases (A, C, T and G) that make up the human DNA and we know that humans carry roughly 20,000 genes. Thanks to this research much has been revealed about the function and structure of genes and their protein products. In addition, new experiments have become possible in which we no longer have to concentrate on a single gene or a single molecule, but instead allow us to study the complete genetic information (the genome) of humans or other organisms.

Bioinformatics

Because of the enormous amount of data generated by this type of experiments, the computer has become indispensable for storing all the complex information on genes, proteins and their functions. On the internet, large databases have become available that are freely accessible. Through smart use of software and computation methods new relationships can be discovered between certain genes and diseases that develop when something is wrong with the corresponding protein. This is the domain of bioinformatics.

Databases and 3D protein structures

In this DNA-lab the students step into the world of CSI, Crime Scene Investigation. In pairs, the students form teams that are charged with investigating a number of ‘suspicious’ proteins that have been found at the scene of a murder. In so doing, the students become acquainted with databases of protein sequences and protein structures. Such databases are essential for genomics research. Subsequently, the students will examine the 3D structure of the ‘guilty’ protein and the potential interactions of that protein with a ligand. The students can experiment with the 3D structure (rotating, zooming in, colouring, etc.) using a programme called Yasara.

Afterwards, the students will receive a CD-rom containing all the teaching material and additional information to further explore the world of genes, proteins and structures.

Note: All the necessary computer equipment is provided with this DNA-lab. There is no need to book the school’s computer room.

Required knowledge

It is advisable that the students are familiar with certain concepts beforehand:

• The student should be familiar with the basic concepts of molecular genetics, such as the roles of DNA, gene, chromosome and heredity.
• The students understand the mutual connection between DNA, genes that are encoded in this DNA and their translation (via mRNA) into proteins.
• The student should know that proteins are made up of amino acids and that the sequence of these amino acids determines secondary structural elements (alpha helices and beta sheets) and the tertiary (three dimensional) structure of the protein and that correct 3D structure is essential for the proper functioning of the protein in the our body.
• The student should know that proteins often bind small molecules (e.g. substrates to enzymes), based on the lock-and-key hypothesis.
• The students should understand that mistakes (mutations) in a protein can cause the ‘key’ not to fit the ‘lock’ anymore, which can result in the development of disease.

The topics mentioned above are also covered in the preparatory lesson, for which teaching material will be provided.

This DNA-lab can be used in both biology and chemistry lessons.