Concluding lesson. Student manual. What kind of protein are you? (Basic)

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1 Concluding lesson Student manual What kind of protein are you? (Basic)

2 Part 1 The hereditary material of an organism is stored in a coded way on the DNA. This code consists of four different nucleotides: adenosine (A), cytosine (C), guanine (G) and thymine (T). In the case of RNA, thymine is replaced by uracil (U). The order in which these nucleotides are linked is called a sequence. Groups of three nucleotides that are next to each other in the sequence are called codons. These codons can be translated into amino acids. But what happens when something changes in the sequence, added or removed? This is called a mutation. There are different kinds of mutations of which five are described below. Missense mutation In a missense mutation 1 nucleotide in a codon changes, which can lead to a completely different amino acid. A missing mutation is a point mutation. Example of a disease: Sickle-cell disease (http://en.wikipedia.org/wiki/sickle-cell_disease) Nonsense mutation The nonsense mutation changes a codon in the sequence of one amino acid into a STOP codon (TAA, TGA, TAG). This causes the cell to stop the addition of more amino acids to the protein. This point mutation finally causes the protein to be shorter. Example of a disease: Thalassemia (http://en.wikipedia.org/wiki/thalassemia) Silent mutation A silent mutation changes a codon of a amino acid into another codon but does not change the amino acid. There is most of the time more then one codon that codes for one amino acid. So sometimes a small change in the DNA sequence has no effect on how a protein is formed. This is why it is called a silent mutation. Deletion mutation The deletion mutation removes a part of the DNA sequence. Due to the fact that the DNA codes is read in groups of three nucleotides, the deletion mutation also changes the manner of reading the rest of the sequence. Example of a disease: Cystic fibrosis (http://en.wikipedia.org/wiki/cystic_fibrosis) Insertion mutation An insertion mutation adds a nucleotide to the DNA sequence. Here too, this has an effect on the groups of three that are formed and therefore the DNA code will be read differently. Example of a disease: Huntington s disease (http://en.wikipedia.org/wiki/huntington%27s_disease) Discover the new world of genomics 2

3 Exercise 1 To gain a better insight in the different mutations one can use the mighty mutation maker. In order to use this program follow the steps below. Go to Enter your name and click on decode. On the left you will see the different mutations. Exercise 1.1 Click on the missense mutation. What happens to your name? Exercise 1.2 Click on the nonsense mutation. What happens to your name? Exercise 1.3 Click on the silent mutation. What happens to your name? Exercise 1.4 Click on the deletion mutation. What happens to your name? Discover the new world of genomics 3

4 Exercise 1.5 Click on the insertion mutation. What happens to your name? Exercise 1.6 Do you still recognize your name after all these different mutations? Scheme 1: Name Result missense mutation Result nonsense mutation Result silent mutation Result deletion mutation Result insertion mutation Discover the new world of genomics 4

5 Part 2 DNA can be translated into amino acids. Amino acids then code for proteins. Different mutations can occur in the DNA that can have effects on the proteins. Five different mutations are missense, nonsense, silent, deletion and insertion mutations. The effects of these mutations are clearly visible on the level of DNA (see Part 1). The effect on the protein sequence is more difficult. This part is very interesting for scientific research, because a disturbed protein function can lead to a wide variety of diseases like Cystic Fibrosis and Alzheimer s disease. Figure 1. Representation of DNA. The DNA consists of genes. These genes code for the amino acid sequence. Amino acid sequences can be transcribed into mrna. mrna can be translated by ribosomes that connects amino acids and thereby makes the protein. The shape of a protein after folding is very important for a protein and its function. This is comparable with the specific shape of a key to fit into a lock. If the key does not fit, the lock won t open. The same goes for proteins; if a protein does not fit into a receptor, there will be no signal transduction. To see how proteins are represented in order to do research, you can look at the following movie: But how do you discover how a proteins folds and what its final shape will look like? Then what are the consequences of mutations in the DNA for the shape of the protein? Now make exercise 2. Discover the new world of genomics 5

6 Exercise 2 To go a step further, you are now going to look at the consequences of mutations for protein folding and the threedimensional structure of a protein. In order to do so, follow the steps below. Make a group of 3 or 4 students Connect the names (first name and surname) of the people in your group Translate the names into an amino acid sequence by using the amino acid alphabet on the right Go to Begin with: >groupname Press Enter On the second line enter the amino acid sequence translation of the names as depicted in the print screen at the bottom of this page Check the Server Policy box Click on Submit Alphabet Amino acid Code A Alanine A B Alanine A C Cysteine C D Aspatic acid D E Glutamic acid E F Phenylalanine F G Glycine G H Histidine H I Isoleucine I J Isoleucine I K Lysine K L Leucine L M Methionine M N Asparagine N O Asparagine N P Proline P Q Glutamine Q R Arginine R S Serine S T Threonine T U Threonine T V Valine V W Tryptophan W X Tryptophan W Y Tyrosine Y Z Tyrosine Y >groupname Amino acid sequence Check box Discover the new world of genomics 6

7 The screen will refresh several times until the calculations are done. This might take a few minutes. You can also manually refresh the page. Click on the name of the group when the program is ready. You can find it under Target id (see the screenshot below). Click Scroll down and make the questions below. Exercise 2.1 Which domains are present in your protein groupname? (Hint: look at the legend) The different domains of a protein all have a certain shape. There is a loop form, a helix (α-helix) with the shape of a spiral staircase and the strand (β-sheet) that looks like a flat plate. The transmembrane helices are special because the protein crosses a cellular membrane. The amino acid sequence of your names determines which domains are present in the protein. What might happen when mutations occur in your name? In order to check the effect of mutations on your protein you are going to test some different mutations on it. Exercise 2.2 Remove the first two letters from each name. What is left of the domains? Discover the new world of genomics 7

8 Exercise 2.3 Remove all the vowels. What is left of the domains? Exercise 2.4 Insert in 5 randomly chosen different places a p (amino acid proline). What happens now with the domains? Exercise 2.5 Finally, insert the name of your teacher at a random position. Does this improve the domain structures or not? Discover the new world of genomics 8

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