Question

Question 1 (Chapter 1 Exercise 2)

One important exercise a bioinformatician performs is to compare amino acid sequences. One reason to make comparisons is to determine the parts of the proteins that are critical for function. These regions are generally conserved within proteins that perform the same duties. Conserved regions are those that have nearly the same amino acid sequences. Proteins that perform the same duties are called homologs and can be found in different species. For example, p53 from humans and p53 from frogs perform the same functions. There are some regions within these proteins that will be similar in both humans and frogs. We call these regions conserved sequences. A multiple sequence alignment allows the bioinformatician to readily line up amino acid sequences of related proteins. The conserved regions are identified in the alignment. For this exercise, perform a multiple sequence alignment of three homologs of cytochrome C. The three homologs are from human, yeast, and dog, and the accession numbers for these sequences are AAA35732, NP_001183974, and 1YCC. The first two sequences can be found in the protein database at the NCBI. The last sequence can be found in the structure database at the Protein Data Bank. ***Print out your multiple sequence alignment result and attach a short paragraph. EXPLAIN how the alignment gives you a clue as to which parts of the cytochrome C protein are MOST important to its function.*** (The function is the same in all three organisms.)

For those of you unfamiliar with NCBI, here are specific instructions:

Go to the NCBI website.

Use the dropdown menu to search in the “Protein” database.

Enter the accession number and click “Search.”

Change the format to FASTA.

Copy the FASTA output into a sequence alignment window of a website that hosts a sequence alignment program. Make sure the header (the line with the > symbol) is placed on top of the sequence within the window.

Repeat for each FASTA output of the remaining two proteins.

Once all three sequences are pasted into the sequence alignment input window, run the program

***please help I starred the portion in the paragraph that I do not know how to answer.

Answer 1

• In the first three pictures, I have shown the retrieved sequences from NCBI and PDB.
• Next, I have used COBALT a tool from NCBI to generate multiple sequence alignment.
• As you could see in Picture 5, the conserved domains have been highlighted in red, and mutations in grey.
• I have also uploaded the Sequence alignment in next picture. You must but also perform the same on your own
• Pertaining to your query about conserved domains
  • As shown in the sequence via Multiple Sequence alignment, positions 5-15, 21-62, 68-87, are the spans that are conserved in all the three sequences. We can assume these are the most important domains and hence are conserved. If a mutation were to occur in these the protein might lose its function and cause lethality in the organism eliminating him from the population.