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Recommended for: AP Biology, Human Genetics, Evolution, Advanced Bio I, (demo for other levels)

Background: 

    Evolution results from changes in our genes.  Some changes are harmful and cause disease while others remain silent or provide variation that may prove helpful over time. There are regions of our genes that are more variable (mutate more rapidly) than other regions. One type of mutation is called a codon expansion that results from strand slippage.  Repeated codon sequences are the cause of many human diseases such as Huntington's and Fragile X.

   This lab activity looks at codon expansions in the "glass" genes of several species of fruit flies. These genes are variable between species. (Some species have many repeats, some have none.) From the data, students will make comparisons of codon expansions present in some of these species to gain an understanding of DNA mutations and their role in disease and evolution.  h

Objectives:

1. To observe the variation between species in a single gene region

2. To compare DNA sequences to search for codon repeats

3. To use Internet software to convert DNA codons to amino acid sequences

4. To introduce students to bioinformatics

Materials:

1. Computer with Internet access

2. Sequence data in digital format (Word or Text document)

3. DataTables

Procedure:

  PART A

Print this page before beginning the activity, but do not close it to maintain the hot links.

1.Open your Internet Browser and go to Dolan DNA Learning Center

2.On the Bioservers page, select SEQUENCE SERVER and press REGISTER

3. Follow the on-screen instructions

4. Record your user name and password for future use.

5. Return to the Bioserver Page and enter username and password

6. Press LOGIN.  This will allow you to store and retrieve entered data.

7. A sequence server and a pop up menu will appear that explains how to find, create and load DNA sequences.

8. Read the information before closing the box to give provide background for the following procedure. Then close the box.

9. Select the choice: CREATE A SEQUENCE

10. Another window comes up with boxes for name and sequence.

11. Refer to the chart below. In the NAME box, type the 1st fly species and gene name (ex. D. melanogaster, gls).

13. Highlight the corresponding sequence from the linked text file in the data table, cut and paste this sequence into the sequence window. Click OK when done.

14. This will display the name of the first sequence on the server page.

15. Repeat this procedure for your assigned fruit fly sequence.

16.  Select the entered GLS sequences and click on COMPARE. (make sure it says Align CLUSTAL W in box to the right).  The next window will show the aligned sequences. This page can be printed for future  reference.

17.  This program has aligned the sequences to make the best match.  Changes in nucleotides are highlighted in yellow.  Dashes are used to indicate areas where a sequence is present in one gene, but not another.

Analysis

1.Scan the sequence alignment between D. melanogaster and your assigned fly.

2.Record any expansion sequences present in your fly but not in melanogaster in the chart below

3.List the repeating codons in the left column.

Expansion Data Table:

Drosophila Codon Expansion

Pool the data for all of the fruit flies in the class data table and compare.

Team Data Table:

NAME

 PART B

These gene sequences can be converted into the sequence of amino acids by using this conversion tool.

1. Copy and paste the sequence for your fruit fly into the DNA data box.

2. Click on TRANSCRIBE to convert to RNA data and then TRANSLATE to convert to amino acid sequences. (Continue to press OK until the pop-up window disappears.)

3. Scan the protein sequence for series of repeated amino acids. A chart of the Genetic Code and a list of abbreviations  for amino acids will allow  you to identify the amino acids in your sequence and their possible codons. 

4. List the amino acid repeats and their possible codons in the protein data table.

Protein Data Table:

Name

Questions   

1. How many codon expansions are present in your assigned fly sequence?

2. Compare and contrast the number and size of expansions between species.

3. Are some of the repeats found  in several species? What sequences are those?

3. What mechanism is responsible for the accumulation of codon repeats through time?

4. How might scientists use this type of data to reconstruct evolutionary history?

5. Do the codon expansions correspond to the amino acid sequences identified  within the protein? Give one example to support your answer.

6. These expansions are found in the coding region of a fruit fly gene. Codon expansions (triplet repeats) are found in many species including humans and are often linked to genetic disorders. Explain why these repeats might effect the functioning of the gene and possibly even neighboring genes.

7. Some changes in DNA sequence even within a gene do not effect protein structure or function, why is that?

Going Further:

Click on the ANALYZE SEQUENCES in the bioserver site which will search the National Center for Biological Information for sequences that identify the organisms. (Although these are short sequences, you will see probabilities for matches.) 

Standards:

A. Students will use scientific inquiry to pose questions, seek answers and develop solutions.

B. Students will access, generate, process and transfer information using appropriate technologies

C. Students will understand and apply scientific concepts, principles and theories

D. Students will apply technological knowledge and skills to use and evaluate products and systems to satisfy human needs

Teacher Notes:

Assign students a particular fly species that they will use to compare to D. melanogaster. Upon completion of the sequence alignment, students with the same assignment may want to compare their results and interpretations.

Extension Activity: Part C